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  Subjects -> MATHEMATICS (Total: 1021 journals)
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    - MATHEMATICS (757 journals)
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MATHEMATICS (757 journals)            First | 1 2 3 4     

Showing 401 - 538 of 538 Journals sorted alphabetically
Journal of K-Theory     Full-text available via subscription  
Journal of Knot Theory and Its Ramifications     Hybrid Journal   (Followers: 1)
Journal of Kufa for Mathematics and Computer     Open Access   (Followers: 1)
Journal of Liquid Chromatography & Related Technologies     Hybrid Journal   (Followers: 7)
Journal of Logical and Algebraic Methods in Programming     Hybrid Journal  
Journal of Manufacturing Systems     Full-text available via subscription   (Followers: 4)
Journal of Mathematical Analysis and Applications     Full-text available via subscription   (Followers: 3)
Journal of mathematical and computational science     Open Access   (Followers: 7)
Journal of Mathematical and Fundamental Sciences     Open Access  
Journal of Mathematical Behavior     Hybrid Journal   (Followers: 2)
Journal of Mathematical Chemistry     Hybrid Journal   (Followers: 3)
Journal of Mathematical Cryptology     Hybrid Journal   (Followers: 1)
Journal of Mathematical Extension     Open Access   (Followers: 3)
Journal of Mathematical Finance     Open Access   (Followers: 7)
Journal of Mathematical Imaging and Vision     Hybrid Journal   (Followers: 6)
Journal of Mathematical Logic     Hybrid Journal   (Followers: 2)
Journal of Mathematical Modelling and Algorithms     Hybrid Journal   (Followers: 1)
Journal of Mathematical Neuroscience     Open Access   (Followers: 9)
Journal of Mathematical Sciences     Hybrid Journal  
Journal of Mathematical Sciences and Applications     Open Access   (Followers: 2)
Journal of Mathematical Sociology     Hybrid Journal   (Followers: 3)
Journal of Mathematics     Open Access  
Journal of Mathematics and Statistics     Open Access   (Followers: 8)
Journal of Mathematics and the Arts     Hybrid Journal   (Followers: 2)
Journal of Mathematics in Industry     Open Access  
Journal of Mathematics Research     Open Access   (Followers: 6)
Journal of Metallurgy     Open Access   (Followers: 7)
Journal of Modern Mathematics Frontier     Open Access  
Journal of Multidisciplinary Modeling and Optimization     Open Access  
Journal of Multivariate Analysis     Hybrid Journal   (Followers: 13)
Journal of Natural Sciences and Mathematics Research     Open Access  
Journal of Nonlinear Analysis and Optimization : Theory & Applications     Open Access   (Followers: 4)
Journal of Nonlinear Mathematical Physics     Hybrid Journal   (Followers: 1)
Journal of Nonlinear Science     Hybrid Journal  
Journal of Numerical Cognition     Open Access  
Journal of Numerical Mathematics     Hybrid Journal   (Followers: 2)
Journal of Optimization     Open Access   (Followers: 4)
Journal of Problem Solving     Open Access   (Followers: 2)
Journal of Progressive Research in Mathematics     Open Access  
Journal of Pseudo-Differential Operators and Applications     Hybrid Journal  
Journal of Pure and Applied Algebra     Full-text available via subscription   (Followers: 4)
Journal of Quantitative Analysis in Sports     Hybrid Journal   (Followers: 8)
Journal of Quantitative Linguistics     Hybrid Journal   (Followers: 6)
Journal of Scientific Computing     Hybrid Journal   (Followers: 18)
Journal of Scientific Research     Open Access  
Journal of Symbolic Computation     Hybrid Journal   (Followers: 1)
Journal of the Australian Mathematical Society     Full-text available via subscription  
Journal of the Egyptian Mathematical Society     Open Access  
Journal of the European Mathematical Society     Full-text available via subscription  
Journal of the Indian Mathematical Society     Hybrid Journal   (Followers: 1)
Journal of the Institute of Mathematics of Jussieu     Hybrid Journal  
Journal of the London Mathematical Society     Hybrid Journal   (Followers: 2)
Journal of the Nigerian Mathematical Society     Open Access   (Followers: 1)
Journal of Theoretical and Applied Physics     Open Access   (Followers: 8)
Journal of Topology and Analysis     Hybrid Journal  
Journal of Transport and Supply Chain Management     Open Access   (Followers: 14)
Journal of Turbulence     Hybrid Journal   (Followers: 7)
Journal of Uncertainty Analysis and Applications     Open Access  
Journal of Universal Mathematics     Open Access  
Journal of Urban Regeneration & Renewal     Full-text available via subscription   (Followers: 10)
Journal of Water and Land Development     Open Access   (Followers: 3)
JRAMathEdu : Journal of Research and Advances in Mathematics Education     Open Access   (Followers: 3)
JURING (Journal for Research in Mathematics Learning)     Open Access   (Followers: 1)
Jurnal Ilmiah AdMathEdu     Open Access  
Jurnal Matematika     Open Access   (Followers: 1)
Jurnal Matematika Integratif     Open Access  
Jurnal Matematika, Sains, Dan Teknologi     Open Access  
Jurnal Natural     Open Access  
Jurnal Pendidikan Matematika Raflesia     Open Access  
Jurnal Penelitian Pembelajaran Matematika Sekolah     Open Access  
Jurnal Penelitian Sains (JPS)     Open Access  
Jurnal Riset Pendidikan Matematika     Open Access  
Jurnal Sains Matematika dan Statistika     Open Access  
Jurnal Tadris Matematika     Open Access  
Jurnal Teknologi dan Sistem Komputer     Open Access  
Kreano, Jurnal Matematika Kreatif-Inovatif     Open Access   (Followers: 5)
Le Matematiche     Open Access  
Learning and Teaching Mathematics     Full-text available via subscription   (Followers: 7)
Lettera Matematica     Hybrid Journal  
Limits : Journal of Mathematics and Its Applications     Open Access   (Followers: 1)
Linear Algebra and its Applications     Full-text available via subscription   (Followers: 18)
Linear and Multilinear Algebra     Hybrid Journal   (Followers: 8)
Lithuanian Mathematical Journal     Hybrid Journal  
LMS Journal of Computation and Mathematics     Free  
Lobachevskii Journal of Mathematics     Open Access  
Logic and Analysis     Hybrid Journal  
Logic Journal of the IGPL     Hybrid Journal  
Logica Universalis     Hybrid Journal  
manuscripta mathematica     Hybrid Journal  
MaPan : Jurnal Matematika dan Pembelajaran     Open Access  
Marine Genomics     Hybrid Journal   (Followers: 2)
Matemáticas, Educación y Sociedad     Open Access  
Matematicheskie Zametki     Full-text available via subscription  
Matematika     Open Access  
Matematychni Studii     Open Access  
Mathematica Eterna     Open Access  
Mathematica Scandinavica     Open Access   (Followers: 1)
Mathematica Slovaca     Hybrid Journal   (Followers: 1)
Mathematical and Computational Forestry & Natural-Resource Sciences     Free  
Mathematical Communications     Open Access  
Mathematical Computation     Open Access   (Followers: 1)
Mathematical Geosciences     Hybrid Journal   (Followers: 3)
Mathematical Medicine and Biology: A Journal of the IMA     Hybrid Journal   (Followers: 1)
Mathematical Methods in the Applied Sciences     Hybrid Journal   (Followers: 3)
Mathematical Methods of Statistics     Hybrid Journal   (Followers: 4)
Mathematical Modelling and Analysis     Open Access   (Followers: 1)
Mathematical Modelling in Civil Engineering     Open Access   (Followers: 5)
Mathematical Modelling of Natural Phenomena     Full-text available via subscription   (Followers: 1)
Mathematical Models and Methods in Applied Sciences     Hybrid Journal   (Followers: 2)
Mathematical Notes     Hybrid Journal  
Mathematical Proceedings of the Cambridge Philosophical Society     Full-text available via subscription   (Followers: 1)
Mathematical Programming Computation     Hybrid Journal   (Followers: 3)
Mathematical Sciences     Open Access  
Mathematical Social Sciences     Hybrid Journal   (Followers: 1)
Mathematical Theory and Modeling     Open Access   (Followers: 13)
Mathematical Thinking and Learning     Hybrid Journal   (Followers: 3)
Mathematics and Statistics     Open Access   (Followers: 5)
Mathematics Education Journal     Open Access   (Followers: 1)
Mathematics Education Research Journal     Partially Free   (Followers: 17)
Mathematics in Science and Engineering     Full-text available via subscription  
Mathematics of Control, Signals, and Systems (MCSS)     Hybrid Journal   (Followers: 4)
Mathematics of Quantum and Nano Technologies     Open Access  
Mathématiques et sciences humaines     Open Access   (Followers: 7)
Mathematische Annalen     Hybrid Journal   (Followers: 1)
Mathematische Nachrichten     Hybrid Journal   (Followers: 1)
Mathematische Semesterberichte     Hybrid Journal  
Mathematische Zeitschrift     Hybrid Journal   (Followers: 1)
MATI : Mathematical Aspects of Topological Indeces     Open Access  
MATICS     Open Access   (Followers: 1)
Matrix Science Mathematic     Open Access  
Measurement Science Review     Open Access   (Followers: 3)
Mediterranean Journal of Mathematics     Hybrid Journal  
Memetic Computing     Hybrid Journal  
Mendel : Soft Computing Journal     Open Access  
Metals and Materials International     Hybrid Journal  
Metascience     Hybrid Journal   (Followers: 1)
Milan Journal of Mathematics     Hybrid Journal  
Mitteilungen der DMV     Hybrid Journal  
MLQ- Mathematical Logic Quarterly     Hybrid Journal  
Monatshefte fur Mathematik     Hybrid Journal  
Moroccan Journal of Pure and Applied Analysis     Open Access   (Followers: 4)
Moscow University Mathematics Bulletin     Hybrid Journal  
MSOR Connections     Open Access   (Followers: 1)
Multiscale Modeling and Simulation     Hybrid Journal   (Followers: 3)
MUST : Journal of Mathematics Education, Science and Technology     Open Access   (Followers: 1)
Nagoya Mathematical Journal     Hybrid Journal  
Nano Research     Hybrid Journal   (Followers: 3)
Nanotechnologies in Russia     Hybrid Journal   (Followers: 1)
Natural Resource Modeling     Hybrid Journal  
New Mathematics and Natural Computation     Hybrid Journal  
Nonlinear Analysis : Modelling and Control     Open Access  
Nonlinear Analysis : Theory, Methods & Applications     Hybrid Journal   (Followers: 1)
Nonlinear Analysis: Hybrid Systems     Hybrid Journal  
Nonlinear Analysis: Real World Applications     Hybrid Journal   (Followers: 2)
Nonlinear Differential Equations and Applications NoDEA     Hybrid Journal  
Nonlinear Engineering     Open Access  
Nonlinear Oscillations     Hybrid Journal   (Followers: 1)
North Carolina Journal of Mathematics and Statistics     Open Access  
North-Holland Mathematical Library     Full-text available via subscription   (Followers: 1)
North-Holland Mathematics Studies     Full-text available via subscription  
North-Holland Series in Applied Mathematics and Mechanics     Full-text available via subscription   (Followers: 1)
Note di Matematica     Open Access  
NTM Zeitschrift für Geschichte der Wissenschaften, Technik und Medizin     Hybrid Journal   (Followers: 4)
Numeracy : Advancing Education in Quantitative Literacy     Open Access  
Numerical Analysis and Applications     Hybrid Journal   (Followers: 1)
Numerical Functional Analysis and Optimization     Hybrid Journal   (Followers: 2)
Numerical Linear Algebra with Applications     Hybrid Journal   (Followers: 4)
Numerical Mathematics : Theory, Methods and Applications     Full-text available via subscription  
Numerische Mathematik     Hybrid Journal  
Open Journal of Discrete Mathematics     Open Access   (Followers: 5)
Open Journal of Modelling and Simulation     Open Access   (Followers: 1)
Open Mathematics     Open Access   (Followers: 1)
Operations Research Letters     Hybrid Journal   (Followers: 11)
Optimization Letters     Hybrid Journal   (Followers: 2)
Optimization Methods and Software     Hybrid Journal   (Followers: 7)
Opuscula Mathematica     Open Access   (Followers: 108)
Order     Hybrid Journal  
ORiON     Open Access  
P-Adic Numbers, Ultrametric Analysis, and Applications     Hybrid Journal  
PAMM : Proceedings in Applied Mathematics and Mechanics     Free   (Followers: 1)
Parallel Processing Letters     Hybrid Journal   (Followers: 3)
Periodica Mathematica Hungarica     Full-text available via subscription   (Followers: 1)
Perspectivas da Educação Matemática     Open Access  
Petroleum Science     Full-text available via subscription   (Followers: 1)
Philosophia Mathematica     Hybrid Journal   (Followers: 1)
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences     Full-text available via subscription   (Followers: 6)
PNA. Revista de Investigación en Didáctica de la Matemática     Open Access  
Polar Science     Hybrid Journal   (Followers: 3)
Positivity     Hybrid Journal  
Prague Bulletin of Mathematical Linguistics, The     Open Access  
Press Start     Open Access  
Prime Number     Full-text available via subscription  
PRIMS     Full-text available via subscription  
Probability in the Engineering and Informational Sciences     Hybrid Journal   (Followers: 1)
Problemy Peredachi Informatsii     Full-text available via subscription  
Proceedings - Mathematical Sciences     Open Access   (Followers: 5)
Proceedings of the American Mathematical Society, Series B     Open Access   (Followers: 1)
Proceedings of the Edinburgh Mathematical Society     Hybrid Journal  
Proceedings of the Institution of Civil Engineers - Engineering and Computational Mechanics     Hybrid Journal   (Followers: 2)
Proceedings of the Latvian Academy of Sciences. Section B: Natural, Exact and Applied Sciences     Open Access  

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Marine Genomics
Journal Prestige (SJR): 0.899
Citation Impact (citeScore): 2
Number of Followers: 2  
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1874-7787
Published by Elsevier Homepage  [3185 journals]
  • Complete genome sequence of the novel alginolytic Psychroserpens sp.
           NJDZ02 isolated from macroalgae collected from King George Island,
    • Abstract: Publication date: Available online 13 September 2019Source: Marine GenomicsAuthor(s): Xiaoqian Gu, Jiang Li, Xuezheng Lin, Yuanyuan Gui, Aihong Pan The general features and genome characteristics of the alginolytic Psychroserpens sp. NJDZ02 isolated from macroalgae collected from King George Island, Antarctica, are described. The sequenced genome is composed of a 4,319,537 bp circular chromosome containing 3699 coding genes including 49 tRNAs and 6 rRNA operons as 16S-23S-5S rRNA. The NJDZ02 genome contains several alginate lyases, which correlate with the high capacity of the strain to degrade sodium alginate. Genome sequencing of NJDZ02 revealed gene candidates of potential interest for use in enzymatic industries or applications in the field of polysaccharide degradation.
  • A review of the potential genes implicated in follicular atresia in
           teleost fish
    • Abstract: Publication date: Available online 8 September 2019Source: Marine GenomicsAuthor(s): Paola González-Kother, Marcelo E. Oliva, Arnaud Tanguy, Dario Moraga In recent years, numerous studies conducted on teleost fish have highlighted the contribution of transcriptomic studies in elucidating the physiological mechanisms underlying the molecular events of oogenesis and follicular atresia, enabling the identification of potential genes and molecular networks that participate in both the reproductive cycle and the process of follicular atresia. Atresia can affect the reproductive potential of females by reducing the healthy eggs that a female can spawn in both aquaculture and wild populations. The substantial diversity of reproductive strategies exhibited by teleost fish has contributed to the difficulty in identifying common genes between species, but a set of core genes has emerged as potential markers for atresia in relation to apoptosis/autophagy, lipid metabolism, oxidative metabolism and other physiological processes similar to those identified in other vertebrates, even mammals. We review the current status of the genes that have been identified in ovaries with atretic oocytes. Our primary goal is to review the current status regarding gene expression during gonadal development and follicular atresia. This information will enable us to understand the factors and expression patterns involved in the follicular atresia of teleost fish.
  • The first transcriptomic resource for the flatworm Triaenophorus nodulosus
           (Cestoda: Bothriocephalidea), a common parasite of holarctic freshwater
    • Abstract: Publication date: Available online 30 August 2019Source: Marine GenomicsAuthor(s): Albina Kochneva, Polina Drozdova, Ekaterina Borvinskaya The order Bothriocephalidea includes worldwide-distributed helminths of marine and freshwater teleost fish. Despite its obvious evolutionary, ecologic and economic importance, there are no transcriptomic, genomic, or proteomic resources available for these organisms. In this data article, we sequenced the transcriptome of a tapeworm, Triaenophorus nodulosus (Pallas, 1781), a common parasite of holarctic freshwater fish. Extracts of total RNA from two different developmental stages (plerocercoid and adult worms) were pooled to create a de novo assembly of the transcriptome, which has been deposited in the NCBI (BioProject PRJNA526283). We also provided functional annotation of the transcripts and predicted the proteome of T. nodulosus. These data will be valuable for studies of molecular evolution and phylogeny of tapeworms, as well as specific adaptations to parasitism in aquatic organisms.
  • Phylotranscriptomics confirms Alveopora is sister to Montipora within the
           family Acroporidae
    • Abstract: Publication date: Available online 26 August 2019Source: Marine GenomicsAuthor(s): Zoe T. Richards, Jose I. Carvajal, Carden C. Wallace, Nerida G. Wilson The genus Alveopora is a scleractinian coral taxon whose phylogenetic classification has recently changed from the family Poritidae to Acroporidae. This change, which was made based on single-locus genetic data, has led to uncertainty about the placement of Alveopora and the ability for deep evolutionary relationships in these groups to be accurately recovered and represented by limited genetic datasets. We sought to characterize the higher-level position of Alveopora using newly available transcriptome data to confirm its placement within Acroporidae and resolve its closest ancestor. Here we present an analysis of a new 2031 gene dataset that confirms the placement of Alveopora within Acroporidae corroborating other single-locus (COI, 16S and ITS) analyses and a mitogenome dataset. We also resolve the position of Alveopora as sister to the genus Montipora. This has allowed the re-interpretation of morphology, and a rediagnosis of the family Acroporidae and the genus Alveopora.
  • Physiological phenotyping of the adult zebrafish heart
    • Abstract: Publication date: Available online 23 August 2019Source: Marine GenomicsAuthor(s): Eric Lin, Sanam Shafaattalab, Jasmine Gill, Bader Al-Zeer, Calvin Craig, Marcel Lamothe, Kaveh Rayani, Marvin Gunawan, Alison Yueh Li, Leif Hove-Madsen, Glen F. Tibbits The zebrafish has proven to be an excellent organism for manipulation of its genome from a long history of transcript down-regulation using morpholino oligimers to more recent genome editing tools such as CRISPR-Cas9. Early forward and reverse genetic screens significantly benefited from the transparency of zebrafish embryos, allowing cardiac development as a function of genetics to be directly observed. However, gradual loss of transparency with subsequent maturation limited many of these approaches to the first several days post-fertilization. As many genes are developmentally regulated, the immature phenotype is not entirely indicative of that of the mature zebrafish. For accurate phenotyping, subsequent developmental stages including full maturation must also be considered.In adult zebrafish, cardiac function can now be studied in great detail due both to the size of the hearts as well as recent technological improvements. Because of their small size, zebrafish are particularly amenable to high frequency echocardiography for detailed functional recordings. Although relatively small, the hearts are easily excised and contractile parameters can be measured from whole hearts, heart slices, individual cardiomyocytes and even single myofibrils. Similarly, electrical activity can also be measured using a variety of techniques, including in vivo and ex vivo electrocardiograms, optical mapping and traditional microelectrode techniques. In this report, the major advantages and technical considerations of these physiological tools are discussed.
  • Comparative de novo assembly and annotation of mantle tissue
           transcriptomes from the Mytilus edulis species complex (M. edulis, M.
           galloprovincialis, M. trossulus)
    • Abstract: Publication date: Available online 12 August 2019Source: Marine GenomicsAuthor(s): Loreen Knöbel, Corinna Breusing, Till Bayer, Virag Sharma, Michael Hiller, Frank Melzner, Heiko Stuckas Mytilus mussels (Mytilus edulis (ME), M. trossulus (MT), and M. galloprovincialis (MG)) are of interest in many fields of marine science and have been used as model in evolutionary research. For instance, they form mosaic hybrid zones or hybrid swarms in areas of secondary contact and hence are suited to address questions related to the evolution of reproductive barriers, adaptive hybridization or speciation. While existing genomic information mostly focuses on single species (ME, MG), this project generated RNA seq data of all three species from allopatric populations, i.e. samples representing genetically pure specimens. We investigated adult mantle tissue (four specimens per species), which is functionally involved in processes such as reproduction or biomineralization. The project provides three assembled transcriptomes (post filtering total transcript numbers for ME: 353339, MT: 437827, MG: 290267) representing genes annotated to at least 40 level 2 GO-terms (number (percentage) of annotated transcripts for ME: 44434 (12.6%), MT: 43960 (10%), MG: 60064 (20.7%)). Annotation showed that the most abundant 40 GO-terms are equally well covered by contigs of the three Mytilus transcriptomes. Therefore, this project lays a basis for evolutionary research by providing candidate genes representing various molecular functions such as reproduction, cellular processes or immune response. The potential of the new transcriptomes to address evolutionary questions is further exemplified by a pilot study on ME and MT transcriptomes that used reciprocal blast to identify 7652 one-to-one orthologue pairs of transcripts.
  • Complete genome sequence of Marinobacter sp. LQ44, a haloalkaliphilic
           phenol-degrading bacterium isolated from a deep-sea hydrothermal vent
    • Abstract: Publication date: Available online 18 July 2019Source: Marine GenomicsAuthor(s): Meixian Zhou, Binbin Dong, Zongze Shao Marinobacter sp. strain LQ44, an alkaliphile and moderate halophile from a deep-sea hydrothermal vent on the East Pacific Rise, is a novel phenol-degrading bacterium that is capable of utilizing phenol as sole carbon and energy sources. Here, we present the complete genome sequence of strain LQ44, which consists of 4,435,564 bp with a circular chromosome, 4164 protein-coding genes, 3 rRNA operons and 50 tRNAs. Genome analysis revealed that strain LQ44 may degrade phenol via meta-cleavage pathway. The LQ44 genome contains multiple genes involved in pH adaptation and osmotic adjustment. Genes related to hydrocarbon degradation, aerobic denitrification and potential industrial important enzymes were also identified from the genome. To our knowledge, this is the first report of a genome sequence of a haloalkaliphilic phenol-degrading bacterium, which will provide insights into the survival of this bacterium under salt-alkali conditions and the potential for biotechnological applications.
  • Characterization of thermally sensitive miRNAs reveals a central role of
           the FoxO signaling pathway in regulating the cellular stress response of
           an extreme stenotherm, Trematomus bernacchii
    • Abstract: Publication date: Available online 12 July 2019Source: Marine GenomicsAuthor(s): Dipali J. Vasadia, Mackenzie L. Zippay, Sean P. Place Despite the lack of an inducible heat shock response (HSR), the Antarctic notothenioid fish, Trematomus bernacchii, has retained a level of physiological plasticity that can at least partially compensate for the effects of acute heat stress. Over the last decade, both physiological and transcriptomic studies have signaled these fish can mitigate the effects of acute heat stress by employing other aspects of the cellular stress response (CSR) that help confer thermotolerance as well as drive homeostatic mechanisms during long-term thermal acclimations. However, the regulatory mechanisms that determine temperature-induced changes in gene expression remain largely unexplored in this species. Therefore, this study utilized next generation sequencing coupled with an in silico approach to explore the regulatory role of microRNAs in governing the transcriptomic level response observed in this Antarctic notothenioid with respect to the CSR. Using RNAseq, we characterized the expression of 125 distinct miRNA orthologues in T. bernacchii gill tissue. Additionally, we identified 12 miRNAs that appear to be thermally responsive based on differential expression (DE) analyses performed between fish acclimated to control (−1.5 °C) and an acute heat stress (+4 °C). We further characterized the functional role of these DE miRNAs using bioinformatics pipelines to identify putative gene targets of the DE miRNAs and subsequent gene set enrichment analyses, which together suggest these miRNAs are involved in regulating diverse aspects of the CSR in T. bernacchii.
  • Complete genome sequence of Antarcticibacterium flavum JB01H24T from an
           Antarctic marine sediment
    • Abstract: Publication date: Available online 11 July 2019Source: Marine GenomicsAuthor(s): Yung Mi Lee, Young Keun Jin, Seung Chul Shin Antarcticibacterium flavum JB01H24T was isolated from a marine sediment of the Ross Sea, Antarctica. Whole-genome sequencing of the strain Antarcticibacterium flavum JB01H24T was achieved using PacBio RS II platform. The resulting complete genome comprised of one closed, complete chromosome of 4,319,074 base pairs with a 40.87% G + C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. It is the first complete genome sequence of the Antarcticibacterium strain.
  • Comparative genomic analysis of three lytic Lactococcus garvieae phages,
           novel phages with genome architecture linking the 936 phage species of
           Lactococcus lactis
    • Abstract: Publication date: Available online 10 July 2019Source: Marine GenomicsAuthor(s): Truong Dinh Hoai, Issei Nishiki, Atushi Fujiwara, Terutoyo Yoshida, Toshihiro Nakai To date, a number of bacteriophages that infect Lactococcus garvieae isolated from marine fish have been identified. However, the evolutionary insight between L. garvieae phages and other viral community have not yet been immersedly investigated. In this study, completed genomic sequence of phage PLgY-30 was obtained, a comparative analysis of three lytic phages, which have been using for phage typing and treatment of L. garvieae infecting marine fish, is conducted. The results revealed that the genomes of lytic phages specific for L. garvieae isolated from diseased marine fish share a high level of homology and almost all proteins are conserved. At genome level, no similarity was detected for either PLgY-30 or PLgY-16, while PLgW-1 shares only very limited homology (1%) with other sequences in Genbank database. In addition, the function of only 35% of ORFs in the PLgY-30 phage genomes could be predicted, demonstrating that it is novel phage. At protein level, lytic phage proteins shared a significant similarity to various proteins of global phage species isolated from dairy fermentation facilities that utilize L. lactis as a primary starter culture, called the 936 phage group. Genome organization and architecture of three lytic phages are also similar to that of the 936 phage group. To our knowledge, this is the first time lytic bacteriophages infecting L. garvieae from marine fish were characterized to genome level.
  • Complete genome sequence of Paracoccus sp. Arc7-R13, a silver
    • Abstract: Publication date: Available online 10 July 2019Source: Marine GenomicsAuthor(s): Shuang Li, Zheng Zhang, Xiaoqian Gu, Xuezheng Lin Paracoccus sp. Arc7-R13, a silver nanoparticles (AgNPs) synthesizing bacterium, was isolated from Arctic Ocean sediment. Here we describe the complete genome of Paracoccus sp. Arc7-R13. The complete genome contains 4,040,012 bp with 66.66 mol% G + C content, including one circular chromosome of 3,231,929 bp (67.45 mol% G + C content), and eight plasmids with length ranging from 24,536 bp to 199,685 bp. The genome contains 3835 protein-coding genes (CDSs), 49 tRNA genes, as well as 3 rRNA operons as 16S-23S-5S rRNA. Based on the gene annotation and Swiss-Prot analysis, a total of 15 genes belonging to 11 kinds, including silver exporting P-type ATPase (SilP), alkaline phosphatase, nitroreductase, thioredoxin reductase, NADPH dehydrogenase and glutathione peroxidase, might be related to the synthesis of AgNPs. Meanwhile, many additional genes associated with synthesis of AgNPs such as protein-disulfide isomerase, c-type cytochrome, glutathione synthase and dehydrogenase reductase were also identified.
  • Genomic differences within the phylum Marinimicrobia: From waters to
           sediments in the Mariana Trench
    • Abstract: Publication date: Available online 10 July 2019Source: Marine GenomicsAuthor(s): Jiao-Mei Huang, Yong Wang Marinimicrobia are widespread from the marine surface to the hadal zone. Major clades of Marinimicrobia have evolved to different ecotypes along with energy gradients, but their genomes in deeper waters and sediments have rarely been studied. Here we obtained 11 Marinimicrobia draft genomes from the water column in the full-ocean depth and the hadal sediments in the Mariana Trench. All the predicted genomic capabilities of the metagenome-assembled genomes (MAGs) are indicative of heterotrophic lifestyle. The MAGs from the hadal depths are distinct from those from the mesopelagic and bathypelagic depths by enrichment of the genes involved in amino acids metabolism and mismatch repair. Compared with the MAGs from waters, those from the sediments were dramatically expanded by acquiring the genes responsible for chemotaxis, mobility and the two-component systems. Marinimicrobia were apparently differentiated in the environments with different depths, organic matters and electronic acceptors. Our results also posit a potential evolutionary relationship between the species inhabiting the waters and sediments, indicating the occurrence of allopatric speciation in Marinimicrobia.
  • Transcriptional profiles of early stage red sea urchins (Mesocentrotus
           franciscanus) reveal differential regulation of gene expression across
    • Abstract: Publication date: Available online 19 June 2019Source: Marine GenomicsAuthor(s): Juliet M. Wong, Juan D. Gaitán-Espitia, Gretchen E. Hofmann The red sea urchin, Mesocentrotus franciscanus, is an ecologically important kelp forest species that also serves as a valuable fisheries resource. In this study, we have assembled and annotated a developmental transcriptome for M. franciscanus that represents eggs and six stages of early development (8- to 16-cell, morula, hatched blastula, early gastrula, prism and early pluteus). Characterization of the transcriptome revealed distinct patterns of gene expression that corresponded to major developmental and morphological processes. In addition, the period during which maternally-controlled transcription was terminated and the zygotic genome was activated, the maternal-to-zygotic transition (MZT), was found to begin during early cleavage and persist through the hatched blastula stage, an observation that is similar to the timing of the MZT in other sea urchin species. The presented developmental transcriptome will serve as a useful resource for investigating, in both an ecological and fisheries context, how the early developmental stages of this species respond to environmental stressors.
  • Genomic analysis of Marinobacter sp. NP-4 and NP-6 isolated from the
           deep-sea oceanic crust on the western flank of the Mid-Atlantic Ridge
    • Abstract: Publication date: Available online 13 June 2019Source: Marine GenomicsAuthor(s): Yinzhao Wang, Xinxu Zhang, Jiahua Wang, Xiang Xiao, Fengping Wang Two Marinobacter sp. NP-4 and NP-6 were isolated from a deep oceanic basaltic crust at North Pond, located at the western flank of the Mid-Atlantic Ridge. These two strains are capable of using multiple carbon sources such as acetate, succinate, glucose and sucrose while take oxygen as a primary electron acceptor. The strain NP-4 is also able to grow anaerobically under 20 MPa, with nitrate as the electron acceptor, thus represents a piezotolerant. To explore the metabolic potentials of Marinobacter sp. NP-4 and NP-6, the complete genome of NP-4 and close-to-complete genome of NP-6 were sequenced. The genome of NP-4 contains one chromosome and two plasmids with the size of 4.6 Mb in total, and with average GC content of 57.0%. The genome of NP-6 is 4.5 Mb and consists of 6 scaffolds, with an average GC content of 57.1%. Complete glycolysis, citrate cycle and aromatics compounds degradation pathways are identified in genomes of these two strains, suggesting that they possess a heterotrophic life style. Additionally, one plasmid of NP-4 contains genes for alkane degradation, phosphonate ABC transporter and cation efflux system, enabling NP-4 extra surviving abilities. In total, genomic information of these two strains provide insights into the physiological features and adaptation strategies of Marinobacter spp. in the deep oceanic crust biosphere.
  • Complete genome sequence of Desulfobacter hydrogenophilus AcRS1
    • Abstract: Publication date: Available online 31 May 2019Source: Marine GenomicsAuthor(s): Angeliki Marietou, Marie B. Lund, Ian P.G. Marshall, Lars Schreiber, Bo Barker Jørgensen Desulfobacter hydrogenophilus strain AcRS1 is a mesophilic sulfate-reducing bacterium isolated from marine sediment. Here we present the complete genome sequence of D. hydrogenophilus AcRS1 which consists of a circular chromosome of 5,105,135 bp length and two plasmids of 45,346 bp and 6889 bp length. The genome data provide insights into the metabolic potential that allows these sulfate-reducing microorganisms to thrive in the cold subseafloor.
  • Complete genome sequence of Paenisporosarcina antarctica CGMCC 1.6503T, a
           marine psychrophilic bacterium isolated from Antarctica
    • Abstract: Publication date: Available online 29 May 2019Source: Marine GenomicsAuthor(s): Jin-Cheng Rong, Yang Liu, Shuang Yu, Lun Xi, Nai-Yu Chi, Qing-Fang Zhang A marine psychrophilic bacterium Paenisporosarcina antarctica CGMCC 1.6503T (= JCM 14646T) was isolated off King George Island, Antarctica (62°13′31″ S 58°57′08″ W). In this study, we report the complete genome sequence of Paenisporosarcina antarctica, which is comprised of 3,972,524 bp with a mean G + C content of 37.0%. By gene function and metabolic pathway analyses, studies showed that strain CGMCC 1.6503T encodes a series of genes related to cold adaptation, including encoding fatty acid desaturases, dioxygenases, antifreeze proteins and cold shock proteins, and possesses several two-component regulatory systems, which could assist this strain in responding to the cold stress, the oxygen stress and the osmotic stress in Antarctica. The complete genome sequence of P. antarctica may provide further insights into the genetic mechanism of cold adaptation for Antarctic marine bacteria.
  • Complete genome of Pseudomonas sp. DMSP-1 isolated from the Arctic
           seawater of Kongsfjorden, Svalbard
    • Abstract: Publication date: Available online 29 May 2019Source: Marine GenomicsAuthor(s): Yin-Xin Zeng, Yi-He Zhang, Jiang-Yong Qu The genus Pseudomonas is highly metabolically diverse and has colonized a wide range of ecological niches. The strain Pseudomonas sp. DMSP-1 was isolated from Arctic seawater (Kongsfjorden, Svalbard) using dimethylsulfoniopropionate (DMSP) as the sole carbon source. To better understand its role in the Arctic coastal ecosystem, the genome of Pseudomonas sp. strain DMSP-1 was completely sequenced. The genome contained a circular chromosome of 6,282,445 bp with an average GC content of 60.01 mol%. A total of 5510 protein coding genes, 70 tRNA genes and 19 rRNA genes were obtained. However, no genes encoding known enzymes associated with DMSP catabolism were identified in the genome, suggesting that novel DMSP degradation genes might exist in Pseudomonas sp. strain DMSP-1.
  • Microbial communities associated with the parasitic copepod
           Lepeophtheirus salmonis
    • Abstract: Publication date: Available online 28 May 2019Source: Marine GenomicsAuthor(s): S. Dalvin, K.O. Skaftnesmo, K. Malde, K.A. Glover, J.S. Leong, B.F. Koop, R.B. Edvardsen, N. Sandlund Lepeophtheirus salmonis is a naturally occurring marine parasite of salmonid fishes in the Northern hemisphere, and a major problem in salmonid aquaculture. In addition to the direct effects on host fish, L. salmonis may act as a vector for diseases. Here, the microbial community of L. salmonis recovered from whole genome shotgun sequencing was compared between lice sampled from both the Atlantic and the Pacific, laboratory-reared and wild lice, in addition to lice displaying resistance towards chemical treatments. The analysis shows clear differences in the metagenomic composition between the Atlantic and the Pacific Ocean, whereas the resistance status of the L. salmonis or the cultivation did not have significant impact.
  • Complete genome sequences of pooled genomic DNA from 10 marine bacteria
           using PacBio long-read sequencing
    • Abstract: Publication date: Available online 23 May 2019Source: Marine GenomicsAuthor(s): Weizhi Song, Torsten Thomas, Richard J. Edwards BackgroundHigh-quality, completed genomes are important to understand the functions of marine bacteria. PacBio sequencing technology provides a powerful way to obtain high-quality completed genomes. However individual library production is currently still costly, limiting the utility of the PacBio system for high-throughput genomics. Here we investigate how to generate high-quality genomes from pooled marine bacterial genomes.ResultsPooled genomic DNA from 10 marine bacteria were subjected to a single library production and sequenced with eight SMRT cells on the PacBio RS II sequencing platform. In total, 7.35 Gbp of long-read data was generated, which is equivalent to an approximate 168× average coverage for the input genomes. Genome assembly showed that eight genomes with average nucleotide identities (ANI) lower than 91.4% can be assembled with high-quality and completion using standard assembly algorithms (e.g. HGAP or Canu). A reference-based reads phasing step was developed and incorporated to assemble the complete genomes of the remaining two marine bacteria that had an ANI > 97% and whose initial assemblies were highly fragmented.ConclusionsTen complete high-quality genomes of marine bacteria were generated. The findings and developments made here, including the reference-based read phasing approach for the assembly of highly similar genomes, can be used in the future to design strategies to sequence pooled genomes using long-read sequencing.
  • Genome of Alcanivorax sp. 24: A hydrocarbon degrading bacterium isolated
           from marine plastic debris
    • Abstract: Publication date: Available online 22 May 2019Source: Marine GenomicsAuthor(s): V. Zadjelovic, M.I. Gibson, C. Dorador, J.A. Christie-Oleza Alcanivorax is an important member of the hydrocarbonoclastic group known for using alkanes and other related compound as their preferred carbon source. Here we report the genomic characteristics of Alcanivorax sp. 24 isolated from plastic marine debris. Its 4,765,873 bp genome, containing 4239 coding sequences, revealed the presence of all genomic features involved in alkane degradation (i.e. two cytochrome P450, three alkane monooxygenases AlkB and two enzymes involved in the degradation of long-chain alkanes AlmA) as well as other relevant enzymes that may play a role in the biodegradation of other polymers such as polyhydroxybutyrate. The genome features and phylogenetic context of these genes provide interesting insight into the lifestyle versatility of Alcanivorax sp. living in the plastisphere of marine plastic debris.
  • Reconstruction and in silico analysis of new Marinobacter adhaerens
           t76_800 with potential for long-chain hydrocarbon bioremediation
           associated with marine environmental lipases
    • Abstract: Publication date: Available online 8 May 2019Source: Marine GenomicsAuthor(s): Erica Mendes Lopes, Camila Cesário Fernandes, Eliana G. de Macedo Lemos, Luciano Takeshi Kishi Marinobacter is a Gammaproteobacterium and member of the family Alteromonadaceae. Some Marinobacter species degrade hydrocarbons and aromatic compounds, raising the possibility of applications in marine bioremediation. Using draft metagenome-assembled genomes from environmental DNA, it was possible to obtain the genome of Marinobacter adhaerens t76_800, from samples obtained during the Tara Oceans expedition. The 4,478,190 bp genome did not contain a plasmid. The genome contained 5580 genes and 49 RNAs. In silico analysis confirmed the presence of genes involved in bioremediation, lipases, as well as defense mechanisms. This microorganism has biotechnological potential and may be useful in bioremediation.
  • Complete genome of a marine bacterium Vibrio chagasii ECSMB14107 with the
           ability to infect mussels
    • Abstract: Publication date: Available online 3 May 2019Source: Marine GenomicsAuthor(s): Xiao Liang, Jin-Song Wang, Yu-Zhu Liu, Li-Hua Peng, Yi-Feng Li, Frederico M. Batista, Deborah M. Power, Lang Gui, Jin-Long Yang Vibrio strains are pervasive in the aquatic environment and may form pathogenic and symbiotic relationships with the host. Vibrio chagasii ECSMB14107 was isolated from natural biofilms and is used as a model to elucidate the role of Vibrio in hard-shelled mussel (Mytilus coruscus) settlement, health and disease. The genome of the Vibrio strain ECSMB14107, comprised of two circular chromosomes that together encompass 5,549,357 bp with a mean GC content of 44.39% was determined. Knowledge about the genome of V. chagasii ECSMB14107 will provide insight into its contribution to mussel development and health.
  • Genomic data mining of an Antarctic deep-sea actinobacterium,
           Janibacter limosus P3-3-X1
    • Abstract: Publication date: Available online 26 April 2019Source: Marine GenomicsAuthor(s): Shiyuan Su, Li Liao, Yong Yu, Jin Zhang, Bo Chen Janibacter limosus P3-3-X1, a psychrotolerant deep-sea actinobacterium isolated from the Southern Ocean, was completely sequenced and analyzed for its biotechnological potential in bioremediation and natural product biosynthesis. The circular genome contained 3.5 Mb with a high GC content of 70.44 mol%. Genomic data mining revealed a gene cluster for degrading phenol and its derivatives, including a multi-component phenol hydroxylase and a meta-cleavage pathway. The strain was shown to grow on phenol as its sole carbon source, supporting the findings of genomic analysis. Many more genes encoding for monooxygenases, dioxygenases and other aromatic compound degradation proteins involved in xenobiotics degradation were detected. Multiple natural product biosynthesis gene clusters were predicted as well. The genome sequencing and data mining provide insights into the bioremediation ability and biosynthetic potential of the Antarctic actinobacterium, and promote further experimental verification and exploration.
  • Microarray analysis of gene expression of Atlantic cod from different
           Baltic Sea regions: Adaptation to salinity
    • Abstract: Publication date: Available online 24 April 2019Source: Marine GenomicsAuthor(s): Magdalena Malachowicz, Roman Wenne The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray. The results showed that a total of 1043 genes were differently expressed between localities. Overall, our results suggested different adaptation patterns to low salinity in the Baltic Sea between cod subpopulations and demonstrated importance of genes involved in cell cycle, lipid metabolism and immune system in this process.
  • The first reference transcriptome assembly of the stalked barnacle,
           Neolepas marisindica, from the Onnuri Vent Field on the Central Indian
    • Abstract: Publication date: Available online 22 April 2019Source: Marine GenomicsAuthor(s): Taewoo Ryu, Seonock Woo, Nayoung Lee Neolepas marisindica (Arthropoda; Scalpellomorpha; Eolepadidae) is a deep-sea stalked barnacle, previously reported as a new species, found along the Central Indian Ridge. It is morphologically distinct from N. zevinae and N. rapanuii, which are found in the Pacific. We sequenced the transcriptome assembly of N. marisindica from individuals collected at a depth of 2022 m off the Onnuri Vent Field on the Central Indian Ridge by video-guided hydraulic grab from the research vessel ISABU (RV ISABU). We sequenced the transcriptome using the Illumina HiSeq X System. De novo assembly and analysis of coding regions predicted 26,201 coding sequences. The reference assembly of N. marisindica will be a valuable resource for future investigations into the ecological characteristics of this species in hydrothermal vent ecosystems. Furthermore, examining the features of hydrothermal vents with functional gene analyses will provide useful information regarding environmental interactions or evolution processes in organisms that inhabit deep-sea hydrothermal vents.
  • First transcriptome assembly of the temperate azooxanthellate octocoral
           Eleutherobia rubra
    • Abstract: Publication date: Available online 20 April 2019Source: Marine GenomicsAuthor(s): Taewoo Ryu, In-Young Cho, Sung-Jin Hwang, Seungshic Yum, Min-Seop Kim, Seonock Woo Eleutherobia rubra (Brundin, 1896) is a temperate asymbiotic octocoral, distributed around Korea, Japan, the west coast of the USA, and northwest Australia. This soft coral is particularly found in the East, West, and South Seas around the Korean Peninsula, so it is useful for investigating the stress responses of corals to rising seawater temperatures around the Korean Peninsula simultaneously and the effects of climate change on coral ecosystems in temperate regions. One individual of E. rubra (Anthozoa: Alcyonacea: Alcyoniidae) was collected around Pohang, South Korea (36°00′17.7”N, 129°35′12.1″E) and extracted total RNA to construct the transcriptome assembly. The Illumina HiSeq3000 platform was used for the transcriptome sequencing and 32,624 coding sequences were predicted by the de novo assembly and analysis of the coding regions. This is the first transcriptome assembly for the genus Eleutherobia. The transcriptome information for E. rubra will be a valuable resource for studying the transcriptomic changes in temperate and cold-water corals in response to environmental stresses.
  • Complete genome sequence of Pseudoalteromonas sp. MEBiC 03485, isolated
           from deep-sea sediment
    • Abstract: Publication date: Available online 18 April 2019Source: Marine GenomicsAuthor(s): Min Seo Jeon, Jeong-Joo Oh, Sang-Il Han, Chulhwan Park, Changsu Lee, Yoon-E Choi Pseudoalteromonas strains are widely distributed in the marine environment and most have attracted considerable interest owing to their ability to synthesize biologically active metabolites. In this study, we report and describe the genome sequence of Pseudoalteromonas sp. MEBiC 03485, isolated from the deep-sea sediment of Pacific Ocean at a depth of 2000 m. The complete genome consisted of three contigs with a total genome size of 4,167,407 bp and a GC content of 40.76 l%, and was predicted to contain 4194 protein-coding genes and 131 non-coding RNA genes. The strain MEBiC 03485 genome was also shown to contain genes for diverse metabolic pathways. Genome analysis revealed that the genome of strain MEBiC 03485 was enriched with genes involved in signal transduction, mobile elements, and cold-adaptation, some of which might improve ecological fitness in the deep-sea environment. These findings improve our understanding of microbial adaptation strategies in deep-sea environments.
  • De novo transcriptome assembly of the digitate morphotype of Briareum
           asbestinum (Octocorallia: Alcyonacea) from the southwest shelf of Puerto
    • Abstract: Publication date: Available online 17 April 2019Source: Marine GenomicsAuthor(s): Liajay Rivera-García, Ramón E. Rivera-Vicéns, Alex J. Veglia, Nikolaos V. Schizas Octocorals have now become the most visually dominant metazoan benthic taxa of most Caribbean reefs, following the precipitous decline of scleractinian corals. Yet taxonomic issues because of their extensive phenotypic plasticity are still abound. Briareum asbestinum one of the iconic octocorals of the shallow Caribbean coral reefs exhibits a biform morphology, the digitate and the encrusting one. The taxonomic status of each form has not been clarified, yet. Until recently, there were few genetic resources for non-model metazoans, however, affordable high-throughput DNA sequencing has removed this hindrance. We present the first transcriptome of the digitate form of Briareum asbestinum from southwest Puerto Rico. We used paired-end sequencing (Illumina NextSeq 500), with a total yield of 159,754,702 raw reads. De novo assembly was performed utilizing a multi-assembler approach generating 371,554 biologically true, non-redundant transcripts. Open reading frame analysis identified 102,839 putative ORFs of which 78,607 were with annotations. BUSCO analysis indicated a total of 96.4% complete orthologous genes from the metazoan dataset. The assembly presented here serves as an important new genomic reference for the Briareum genus that will facilitate future population and phylogenetic studies aiming to better understand the molecular basis of phenotypic plasticity exhibited throughout the genus.
  • Complete genome sequence of Hahella sp. KA22, a
           prodigiosin-producing algicidal bacterium
    • Abstract: Publication date: Available online 12 April 2019Source: Marine GenomicsAuthor(s): Jiarong Feng, Zhong Hu, Hui Wang Hahella sp. KA22 is a gamma-proteobacteria bacterium that belongs to the family Hahellaceae and order Oceanospirillales. Strain KA22 is capable of producing prodigiosin, which is a compound with algicidal activity. It is for this reason that further investigation of the genome of strain KA22 will help in revealing the prodigiosin producing mechanism and its ecological functions. In this study, we sequenced and annotated the complete genome of Hahella sp. KA22, the second complete genome sequence of prodigiosin-producing bacteria in the family Hahellacaeae. The genome of strain KA22 is 6,927,416 base pairs in size, contains one chrome with no plasmid and predicted to contain 6167 protein-coding genes and 86 RNA-only encoding genes. Genomic analysis of Hahella sp. KA22 reveals that this strain of bacteria can be used for biological elimination or control of harmful algal blooms (HABs).
  • De Novo assembly and characterisation of the greentail prawn (Metapenaeus
           bennettae) hepatopancreas transcriptome – identification of stress
           response and detoxification transcripts
    • Abstract: Publication date: Available online 12 April 2019Source: Marine GenomicsAuthor(s): Emily K. Armstrong, Adam D. Miller, Julie A. Mondon, Paul A. Greenfield, Sarah A. Stephenson, Mun Hua Tan, Han Ming Gan, Sharon E. Hook Crude oil is a key contaminant in aquatic environments entering via natural and anthropogenic sources, causing toxicity in marine organisms. Traditionally, biomarkers have been utilised to determine crude oil exposure and effects in aquatic organisms, however advances in genomic technologies has led to increased adoption of transcriptomic approaches for identifying response and detoxification pathways following contaminant exposure. This study presents the first transcriptome for the greentail prawn (Metapenaeus bennettae), a commercially targeted benthic decapod crustacean from eastern and south-eastern Australia. The Trinity generated de novo assembly, after redundancy clustering, resulted in 86,401 contigs, of these 22,252 displayed strong homology to transcripts in the NCBI's non-redundant protein, Swiss-Prot and TrEMBL databases. Furthermore, Gene Ontology was assigned to 15,079 annotated contigs and KEGG Orthology was identified for 1318 annotated contigs. Transcripts encoding common biomarkers utilised to determine crude oil exposure were identified, including those for detoxification phase I and II enzymes; with 40 transcripts encoding for members of the cytochrome P450 gene family and 8 transcripts encoding glutathione S-Transferases (GSTs). Transcripts encoding oxidative stress enzymes including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and metallothionein (MT) were identified, as well as stress induced proteins including crustacean hyperglycemic hormone (CHH) and heat shock proteins (Hsps). The annotated transcriptome of the greentail prawn and the identification of detoxification and stress response transcripts, provides a necessary resource for future studies geared toward characterising differential transcriptomic patterns and molecular pathways after exposure to crude oil in this and other crustacean species of environmental and commercial importance.
  • Characterization, complete genome and proteome of a bacteriophage
           infecting a coral-derived Vibrio strain
    • Abstract: Publication date: Available online 6 April 2019Source: Marine GenomicsAuthor(s): Xinyuanyuan Sun, Sijun Huang, Lijuan Long A virulent bacteriophage, vB_VspP_SBP1 (SBP1 hereafter), which infects a coral-derived Vibrio strain, SCSIO30225, was isolated and characterized in morphological, physiological, genomic and proteomic aspects. Vibrio strain SCSIO30225 was isolated from a piece of coral tissue collected from the Sanya Bay, the South China Sea, which is most closely related to V. owensii based on 16S rRNA sequence similarity. SBP1 has an isometric head and a short tail, indicating it is a member of the Podoviridae virus family. The latent period is ~20 min and the burst size is 193 pfu per cell. SBP1 could not infect other 9 Vibrio strains for host range testing. The 78,071 bp genome contains 112 open reading frames (ORFs) and 4 tRNAs, and 35 of the ORFs could be functionally annotated. The gene content of SBP1 shows explicit features of N4-like phages. Phylogenetic analysis based on virion-encapsulated RNA polymerase sequence indicated that SBP1 is distantly related to other known N4-like phages. Proteomic analysis identified 13 virion proteins including the virion-encapsulated RNA polymerase, is the hallmark feature of N4-like phages.
  • Metagenomic assessment of body surface bacterial communities of the sea
           urchin, Tripneustes gratilla
    • Abstract: Publication date: Available online 5 April 2019Source: Marine GenomicsAuthor(s): M. Brink, C. Rhode, B.M. Macey, K.W. Christison, R. Roodt-Wilding Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.
  • Comparative genomic analyses reveal trehalose synthase genes as the
           signature in genus Methanoculleus
    • Abstract: Publication date: Available online 30 March 2019Source: Marine GenomicsAuthor(s): Sheng-Chung Chen, Chieh-Yin Weng, Mei-Chin Lai, Hideyuki Tamaki, Takashi Narihiro To date, the only methanoarchaea isolated directly from methane hydrate bearing sediments were Methanoculleus submarinus Nankai-1T and Methanoculleus sp. MH98A. Here, we provide the genome of Methanoculleus taiwanensis CYW4T isolated from the deep-sea subseafloor sediment at the Deformation Front offshore southwestern Taiwan, where methane hydrate deposits are likely located. Through comparative genomics analyses of nine Methanoculleus strains from various habitats, 2–3 coding genes for trehalose synthases were found in all nine Methanoculleus genomes, which were not detected in other methanogens and are therefore suggested as a signature of genus Methanoculleus among methane-producing archaea. In addition, the structural genes adjacent to trehalose synthase genes are comprised of the signaling module of Per-Arnt-Sim (PAS) domain-containing proteins, Hsp20 family proteins, arabinose efflux permeases and multiple surface proteins with fasciclin-like (FAS) repeat. This indicates that trehalose synthase gene clusters in Methanoculleus might play roles in the response to various stresses and regulate carbon storage and modification of surface proteins through accumulation of trehalose. The non-gas hydrate-associated Methanoculleus strains harbor carbon-monoxide dehydrogenase (cooS/acsA) genes, which are important for the conversion of acetate to methane at the step of CO oxidation/CO2 reduction in acetoclastic methanogens and further implies that these strains may be able to utilize CO for methanogenesis in their natural habitats. In addition, both genomes of M. bourgensis strains MS2T and MAB1 harbor highly abundant transposase genes, which may be disseminated from microbial communities in their habitats, sewage treatment plants and biogas reactors, which are breeding grounds for antibiotic resistance. Through comparative genomic analyses, we gained insight into understanding the life of strictly anaerobic methane-producing archaea in various habitats, especially in methane-based deep-sea ecosystems.
  • Two reads to rule them all: Nanopore long read-guided assembly of the
           iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888),
           mitochondrial genome and the challenges of AT-rich mitogenomes
    • Abstract: Publication date: Available online 28 March 2019Source: Marine GenomicsAuthor(s): Han Ming Gan, Stuart M. Linton, Christopher M. Austin Despite recent advances in sequencing technology, a complete mitogenome assembly is still unavailable for the gecarcinid land crabs that include the iconic Christmas Island red crab (Gecarcoidea natalis) which is known for its high population density, annual mass breeding migration and ecological significance in maintaining rainforest structure. Using sequences generated from Nanopore and Illumina platforms, we assembled the complete mitogenome for G. natalis, the first for the genus and only second for the family Gecarcinidae. Nine Nanopore long reads representing 0.15% of the sequencing output from an overnight MinION Nanopore run were aligned to the mitogenome. Two of them were>10 kb and combined are sufficient to span the entire G. natalis mitogenome. The use of Illumina genome skimming data only resulted in a fragmented assembly that can be attributed to low to zero sequencing coverage in multiple high AT-regions including the mitochondrial protein-coding genes (NAD4 and NAD5), 16S ribosomal rRNA and non-coding control region. Supplementing the mitogenome assembly with previously acquired transcriptome dataset containing high abundance of mitochondrial transcripts improved mitogenome sequence coverage and assembly reliability. We then inferred the phylogeny of the Eubrachyura using Maximum Likelihood and Bayesian approaches, confirming the phylogenetic placement of G. natalis within the family Gecarcinidae based on whole mitogenome alignment. Given the substantial impact of AT-content on mitogenome assembly and the value of complete mitogenomes in phylogenetic and comparative studies, we recommend that future mitogenome sequencing projects consider generating a modest amount of Nanopore long reads to facilitate the closing of problematic and fragmented mitogenome assemblies.
  • De novo assembly and characterization of the transcriptome of the northern
           mauxia shrimp Acetes chinensis
    • Abstract: Publication date: Available online 26 March 2019Source: Marine GenomicsAuthor(s): Hao Huang, Zengpeng Li, Mingliang Chen Northern mauxia shrimp Acetes chinensis, a major fished shrimp in East Asia, serves as an important marine resource in food industry. Here, we collected wild A. chinensis samples and conducted RNA-Seq experiment using different body parts to obtain the transcriptome profile using Illumina HiSeq technology. After de novo assembly, 63,396 transcripts were obtained, and 41,898 transcripts were functionally annotated in reference databases. We further identified a number of well-known transcription factors that are possibly associated with environmental changes. This transcriptome dataset could be immediately used for gene discovery and functional characterization. Our study will shed light on the investigation of molecular adaption of A. chinensis to the changing marine environment.
  • Identification of alternative oxidase encoding genes in Caulerpa
           cylindracea by de novo RNA-Seq assembly analysis
    • Abstract: Publication date: Available online 25 March 2019Source: Marine GenomicsAuthor(s): Ercan Selçuk Ünlü, Ömer Can Ünüvar, Meryem Aydın Alternative oxidases (AOX) are defined in plants, fungi and algae. The main function of AOX proteins has been described for electron flow through electron transport chain and regulation of mitochondrial retrograde signaling pathway. The roles of AOX proteins have been characterized in reproduction and resistance against oxidative stress, cold stress, starvation, and biotic attacks. Caulerpa cylindracea is an invasive marine green alga. Although the natural habitats of the species are Australia coasts, the impact of the invasion has been monitored through the Mediterranean Sea and the Aegean Sea. C. cylindracea species have advantages against others by showing higher resistance to stress conditions such as cold, starvation, pathogen attacks and by their capability of sexual and vegetative reproduction. Comparing the advantages of C. cylindracea over the niche and defined functional roles of mitochondrial AOX proteins, it is evident that AOX proteins are likely involved in developing those advantageous skills in C. cylindracea. However, there is limited data about biochemical and molecular mechanisms that take part in stress resistance and invasion characteristics. We aimed to identify mitochondrial alternative oxidase encoding genes in C. cylindracea while annotating whole transcriptome data for the species. Samples were collected from Seferihisar/İzmir. Transcriptome analysis from pooled RNA samples revealed 47,400 assembled contigs represented by 33,340 unigenes. Using standalone Blast analysis, we were able to identify two alternative oxidase encoding genes.Graphical abstractUnlabelled Image
  • Transcriptome profiling of the meristem tissue of Saccharina japonica
           (Phaeophyceae, Laminariales) under severe stress of copper
    • Abstract: Publication date: Available online 23 March 2019Source: Marine GenomicsAuthor(s): Yurong Zhang, Xuemei Wang, Tifeng Shan, Shaojun Pang, Nianjun Xu Copper (Cu) is an essential metal involved in many physiological processes of living organisms. However, beyond a certain threshold, Cu can become highly toxic. For instance, in the summer sporeling production of the economic kelp Saccharina japonica, the excess Cu accidently released from the low-quality alloys of the refrigerating machine was deadly to the seedlings and led to the failure of hatchery operations. However, the molecular basis underlying high toxicity of Cu remains unclear. In this study, juvenile sporophytes were cultured in seawater containing different concentrations of Cu2+ (10, 100, and 200 μg L−1). Bleaching was observed in the meristem of individuals in the 100 and 200 μg L−1 treatment groups on the third day, indicating that Cu has caused severe harm at these concentrations. RNA-Seq was used to profile transcriptomic changes under different Cu2+ concentrations. Compared with the control, the number of differentially expressed genes (DEGs) was 11,350 (4944 up- and 6406 down-regulated) in the 200 μg L−1 treatment group and 2868 (1075 up- and 1793 down-regulated) in the 100 μg L−1 treatment group, whereas much fewer DEGs were detected in the 10 μg L−1 treatment group. Genes coding for glutathione-S-transferase and vanadium-dependent bromoperoxidase and iodoperoxidase were found to be remarkably regulated, especially in the 200 μg L−1 treatment group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that only down-regulated DEGs were enriched. There were 45 enriched GO terms and four enriched KEGG pathways common to the 100 and 200 μg L−1 treatment groups, which were associated with diverse essential biological processes such as photosynthesis, protein synthesis, redox activity, and metabolism and biosynthesis of functional biomolecules, among others. Suppression of these biological processes at the transcriptional level likely contributes to the observed high toxicity of Cu2+ in S. japonica.
  • Complete genome sequence of Flavobacterium arcticum SM1502T, exhibiting
           adaption to the Arctic marine salty environment
    • Abstract: Publication date: Available online 15 March 2019Source: Marine GenomicsAuthor(s): Yi Li, Bai-Lu Tang, Xue-Bing Ren, Yan-Ru Dang, Lin-Lin Sun, Xi-Ying Zhang, Xiu-Lan Chen, Qi-Long Qin, Peng Wang Flavobacterium arcticum SM1502T, isolated from the surface seawater of King's Fjord, Svalbard, Arctic, is an aerobic, non-flagellated, rod-shaped and yellow-pigmented bacterium belonging to the family Flavobacteriaceae. It is the first isolated Arctic Flavobacterium bacterium. To date, no genomes of Flavobacterium species isolated from the Arctic region have been sequenced. Here, we reported the complete genomic compositions and metabolic features of F. arcticum SM1502T. The genome consists of 2,970,356 bp with an average GC content of 35.0%. A total of 2652 protein-coding sequences and 50 RNA genes were identified in the genome. SM1502T had lower protein pIs with higher ratios of acidic residues to basic residues compared to the relative bacteria and contains genes related to iron transport and organic osmoprotectant uptake, which could maintain cellular osmotic balance. These related genes and protein pI characteristics indicated that SM1502T has high salt tolerance and could accommodate the changing Arctic salty environments.
  • Genomic discovery of ion channel genes in the central nervous system of
           the lamprey Petromyzon marinus
    • Abstract: Publication date: Available online 14 March 2019Source: Marine GenomicsAuthor(s): Adam J. Northcutt, Ryan A. Hough, Alexander N. Frese, Andrew D. McClellan, David J. Schulz The lamprey is a popular animal model for a number of types of neurobiology studies, including organization and operation of locomotor and respiratory systems, behavioral recovery following spinal cord injury (SCI), cellular and synaptic neurophysiology, comparative neuroanatomy, neuropharmacology, and neurodevelopment. Yet relatively little work has been done on the molecular underpinnings of nervous system function in lamprey. This is due in part to a paucity of gene information for some of the most fundamental proteins involved in neural activity: ion channels. We report here 47 putative ion channel sequences in the central nervous system (CNS) of larval lampreys from the predicted coding sequences (CDS) discovered in the P. marinus genome. These include 32 potassium (K+) channels, six sodium (Na+) channels, and nine calcium (Ca2+) channels. Through RT-PCR, we examined the distribution of these ion channels in the anterior (ARRN), middle (MRRN), and posterior (PRRN) rhombencephalic reticular nuclei, as well as the spinal cord (SC). This study lays the foundation for incorporating more advanced molecular techniques to investigate the role of ion channels in the neural networks of the lamprey.
  • Extremophile deep-sea viral communities from hydrothermal vents:
           Structural and functional analysis
    • Abstract: Publication date: Available online 9 March 2019Source: Marine GenomicsAuthor(s): Hugo G. Castelán-Sánchez, Itzel Lopéz-Rosas, Wendy A. García-Suastegui, Raúl Peralta, Alan D.W. Dobson, Ramón Alberto Batista-García, Sonia Dávila-Ramos Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome.
  • Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that
           infects Pseudoalteromonas sp. strain H6
    • Abstract: Publication date: Available online 7 March 2019Source: Marine GenomicsAuthor(s): René Kallies, Bärbel Kiesel, Matthias Schmidt, Nawras Ghanem, Jakob Zopfi, Jörg Hackermüller, Hauke Harms, Lukas Y. Wick, Antonis Chatzinotas Pseudoalteromonas is a bacterial genus widely distributed in marine ecosystems. We present the genome characterization of the lytic Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. The virus and its host were both isolated from seawater collected from the North Sea near the island Helgoland, Germany, in the 1970s. The virus particle consists of a ~56 nm diameter icosahedral capsid and a short tail with a length of ~15 nm. The linear dsDNA genome has a size of 36,753 bp and a GC content of 45%. Genome organization was related to P22-like viruses with approximately 40% nucleotide identity to other P22-like viruses over the whole genome. These findings, together with the phylogenetic analysis, suggest Pseudoalteromonas virus vB_PspP-H6/1 is a marine P22-like virus. The study of such viruses originating from a host so far not known for P22-like viruses will extend the information about origin and evolution of P22-like viruses.
  • Comparative genome analysis provides novel insight into the interaction of
           Aquimarina sp. AD1, BL5 and AD10 with their macroalgal host
    • Abstract: Publication date: Available online 6 March 2019Source: Marine GenomicsAuthor(s): Jennifer Hudson, Vipra Kumar, Suhelen Egan The Aquimarina genus is widely distributed throughout the marine environment, however little is understood regarding its ecological role, particularly when in association with eukaryotic hosts. Here, we examine the genomes of two opportunistic pathogens, Aquimarina sp. AD1 and BL5, and a non-pathogenic strain Aquimarina sp. AD10, that were isolated from diseased individuals of the red alga Delisea pulchra. Each strain encodes multiple genes for the degradation of marine carbohydrates and vitamin biosynthesis. These traits are hypothesised to promote nutrient exchange between the Aquimarina strains and their algal host, facilitating a close symbiotic relationship. Moreover, each strain harbours the necessary genes for the assembly of a Type 9 Secretion System (T9SS) and the associated gliding motility apparatus. In addition to these common features, pathogenic strains AD1 and BL5, encode genes for the production of flexirubin type pigments and a number of unique non-ribosomal peptide synthesis (NRPS) gene clusters, suggesting a role for these uncharacterised traits in virulence. This study provides valuable insight into the potential ecological role of Aquimarina in the marine environment and the complex factors driving pathogenesis and symbiosis in this genus.
  • Comparative transcriptome analysis reveals expression signatures of albino
           Russian sturgeon, Acipenseriformes gueldenstaedtii
    • Abstract: Publication date: Available online 6 March 2019Source: Marine GenomicsAuthor(s): Yiwen Gong, Mou Hu, Shijian Xu, Bin Wang, Chunlin Wang, Xidong Mu, Peng Xu, Yanliang Jiang Albinism is a genetically inherited condition that is caused by a series of genetic abnormalities leading to a reduction in melanin production. Russian sturgeon is one of the most valuable freshwater fish species worldwide, and albino individuals have been found in fish farms. Due to its complicated genome and scarce genome-wide genetic resources, the underlying molecular basis of albinism in Russian sturgeon is unknown. In the present study, we first generated transcriptome profile of Acipenser gueldenstaedtii using pooled tissues, which provided reliable reference sequences for future molecular genetic studies. A total of 369,441 contigs were assembled, corresponding to 32,965 unique genes. A comparative analysis of the transcripts from the skin of albino and wildtype individuals was conducted afterwards. A total of 785 unique genes were differentially expressed, including the upregulation of 385 genes and the downregulation of 400 genes in albino individuals. The expression pattern of 16 selected differentially expressed genes was validated using qRT-PCR. Additional annotation, GO enrichment analysis and gene pathway analysis indicated that the melanogenesis pathway may be interrupted in albinism. Eight potential causative genes that were highly likely to be responsible for sturgeon albinism were identified, including Dct, Tyrp1b, Slc45a2, Ctns, Pmela, Pmelb, Cd63, and Bloc1s3, which were found to be significantly down-regulated in albino Russian sturgeon. Moreover, a sliding window analysis of the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) ratios indicated that seven out of the eight genes underwent positive selection during evolution. Our results provide a valuable basis for understanding the molecular mechanism of albinism in fish species and will facilitate future genetic selection and breeding of sturgeon with market-favored traits in aquaculture.
  • Complete genome sequence of a novel aerobic denitrifying strain,
           Pseudomonas monteilii CY06
    • Abstract: Publication date: Available online 26 February 2019Source: Marine GenomicsAuthor(s): Qingshan Ma, Yali Cai, Zengguo He A novel aerobic denitrifying isolate CY06 was obtained from the Western Pacific Ocean, and it was identified as Pseudomonas monteilii. In this study, we present the complete genome sequence of strain CY06. The genome has one circular chromosome of 5,774,879 bp, with an average G + C content of 61.00%, and 3319 coding sequences. According to the annotation analysis, strain CY06 encodes 22 proteins related to nitrogen metabolism. It is found that CY06 has promising denitrification capacity, revealing its potential for practical use regarding N-removal applications.
  • First de-novo transcriptome assembly, annotation and expression profiles
           of a freshwater snail (Semisulcospira coreana) fed with chlorella
    • Abstract: Publication date: Available online 20 February 2019Source: Marine GenomicsAuthor(s): Sang Yoon Lee, Sang-Min Lee, Yi Kyung Kim The aim of this study was to develop the transcriptome resource of Semisulcospira coreana that would support development of commercial feeds and physiological studies. We compared mRNA expression in S. coreana to determine gene transcripts that were differentially regulated responding two feeding conditions (with or without chlorella). A total of 13.1 G raw reads were obtained and assembled using the CLC Genomics Workbench v 11.0, resulting in 134,402 transcripts with an average length of 694 bp and N50 of 1058 bp. Subsequently, we performed functional gene annotations using BLASTx NR, Gene Ontology (GO), InterProScan, and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified differentially expressed antioxidant-related genes and chlorophyllase (CLH) between the control and experimental groups. This data provides the first insight into the physiological response of S. coreana to chlorella ingestion at the transcriptome level and will be the basis for the study of S. coreana gene resources.
  • Diatom genes originating from red and green algae: Implications for the
           secondary endosymbiosis models
    • Abstract: Publication date: Available online 19 February 2019Source: Marine GenomicsAuthor(s): A.A. Morozov, Yuri P. Galachyants Previous phylogenomic analyses of diatoms have discovered some plastid-targeted genes apparently coming from green algae. Number of these genes varied from less than a half of EGT-compatible genes to an overwhelming majority, and their presence was treated as an evidence of cryptic green plastid. We have performed such an analysis with a novel weighted approach on an extended dataset of diatom genomes and proteomes. Approximately equal evidence was found for red and green algal origins for diatoms genes. Considering that very similar results were obtained on other secondary photosynthetic groups whose endosymbioses were independent from that of the diatom ancestors, we consider the serial plastid replacements unparsimonious. A better explanation of these data can be provided by the shopping bag model, where a future host switches numerous endosymbionts and acquires some genes from each of them. Eventually the host loses the ability to replace endosymbionts (e.g. through the loss of phagotrophy) and whatever symbiont was present at the moment gets fixed and reduced to an organelle.
  • Metatranscriptomics of the bacterial community in response to atmospheric
           deposition in the Western North Pacific Ocean
    • Abstract: Publication date: Available online 17 February 2019Source: Marine GenomicsAuthor(s): Shangjin Tan, Shun Yan Isaac Cheung, Tung-Yuan Ho, Hongbin Liu Atmospheric deposition represents a major vector of both macro- and micro-nutrients to the oligotrophic open oceans, potentially imposing a profound impact on the functioning of the microbial community. Whereas bacterial responses to atmospheric deposition are being studied at the community level, corresponding functional changes are essentially unknown. Here we conducted a microcosm experiment coupled with metatranscriptomic analyses to elucidate taxonomic and functional profiles of the bacterial community in response to East Asian aerosols in the Western North Pacific Ocean (WNPO). While the abundance of heterotrophic bacteria showed a minor change, cyanobacterial cell count number decreased dramatically, with Prochlorococcus and Synechococcus counts reduced by 83.2% and 21.5% in the aerosol treatment in relation to the control. Expression of transcripts related with Prochlorococcus, Synechococcus, Trichodesmium and Crocosphaera both were lower in the treatment (5.7%, 2.3%, 0.5% and 0.02%, respectively) than in the control (18.6%, 2.7%, 9.8% and 0.14%, respectively). Aerosol addition led to an increase in transcripts involved in iron metabolism (tonB, feoB, irr, exbB), indicating Fe limitation. Heavy metal toxicity was evidenced by an elevated expression of resistance genes, such as czcC, czcB, czcA and a probable Co/Zn/Cd efflux protein, and a range of genes functioning against oxidative stress. Our findings provide insights into an inhibitory effect of high-flux East Asian aerosols on cyanobacteria in the WNPO likely due to Fe scavenging and heavy metal toxicity.
  • Characterization of the salmon louse Lepeophtheirus salmonis miRNome:
    • Abstract: Publication date: Available online 14 February 2019Source: Marine GenomicsAuthor(s): Gustavo Núñez-Acuña, Cristian Gallardo-Escárate The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L. salmonis, including precursors and variants. The most abundant and over-expressed miRNAs belonged to the bantam, mir-100, mir-1, mir-263a and mir-276 families, while the most differentially expressed mRNAs corresponded to genes related to reproduction and other biological processes involved in cell-differentiation. Target analyses revealed that the most up-regulated miRNAs in males can act by inhibiting the expression of genes related to female differentiation such as vitellogenin genes. Target prediction and expression patterns suggested a pivotal role of miRNAs in the reproductive development of L. salmonis.
  • De novo transcriptome assembly and gene expression profile of thermally
           challenged green abalone (Haliotis fulgens: Gastropoda) under acute
           hypoxia and hypercapnia
    • Abstract: Publication date: Available online 1 February 2019Source: Marine GenomicsAuthor(s): Miguel A. Tripp-Valdez, Lars Harms, Hans O. Pörtner, M. Teresa Sicard, Magnus Lucassen Transcriptional regulation constitutes a rapid response of marine organisms facing stressful environmental conditions, such as the concomitant exposure to warming, ocean acidification and hypoxia under climate change. In previous studies, we investigated whole-organism physiological patterns and cellular metabolism in gill and muscle of the marine gastropod Haliotis fulgens in response to increasing temperature (18 °C to 32 °C at +3 °C per day) under hypoxia (50% air saturation), hypercapnia (1000 μatm pCO2) and both factors combined. Here, we report investigations of the molecular responses of H. fulgens to temperature and identify mechanisms concomitantly affected by hypoxia and hypercapnia. A de novo transcriptome assembly with subsequent quantitative PCR and correlation network analysis of genes involved in the molecular response were used to unravel the correlations between gene expression patterns under the different experimental conditions. The correlation networks identified a shift from the expression of genes involved in energy metabolism (down-regulated) to the up-regulation of Hsp70 during warming under all experimental conditions in gill and muscle, indicating a strong up-regulation of damage prevention and repair systems at sustained cellular energy production. However, a higher capacity for anaerobic succinate production was evicted in gill, matching with observations from our previous studies indicating succinate accumulation in gill but not in muscle. Additionally, warming under hypoxia and hypercapnia kept mRNA levels of citrate synthase in both tissues unchanged following a similar pattern as muscle enzyme capacity from a previous study, suggesting an emphasis on maintaining rather than down-regulating mitochondrial activity.
  • Single-cell amplified genomes of two uncultivated members of the
           deltaproteobacterial SEEP-SRB1 clade, isolated from marine sediment
    • Abstract: Publication date: Available online 25 January 2019Source: Marine GenomicsAuthor(s): Caitlin Petro, Lara M. Jochum, Lars Schreiber, Ian P.G. Marshall, Andreas Schramm, Kasper U. Kjeldsen The SEEP-SRB1 is a diverse clade of sulfate reducing bacteria affiliated with the deltaproteobacterial family Desulfobacteraceae. Here we report the draft genome sequences of two single cells belonging to the SEEP-SRB1 clade, isolated from marine sediment in Aarhus Bay, Denmark, by fluorescence activated cell sorting (FACS). The draft genomes measure 2.12 Mb and 0.46 Mb, with GC contents of 45% and 42%. Phylogenetic placement of the 16S rRNA genes places the SAGs within the subgroups SEEP-SRB1e and SEEP-SRB1d. While these subgroups are thought to play a role in non-methane hydrocarbon degradation, there is little genomic information available to confirm their metabolic function. As such, these novel single-cell amplified genomes provide valuable insight into the metabolic potential of this prevalent subseafloor clade.
  • Complete genome sequence of Bradymonas sediminis FA350T, the first
           representative of the order Bradymonadales
    • Abstract: Publication date: Available online 18 January 2019Source: Marine GenomicsAuthor(s): Shuo Wang, Da-Shuai Mu, Wei-Shuang Zheng, Zong-Jun Du Bradymonas sediminis FA350T (=DSM 28820T = CICC 10904T) is a Gram-negative, rod-shaped and facultatively anaerobic bacterium isolated from coastal sediments from the Xiaoshi Island, Weihai, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that that strain FA350T belonged to a novel bacterial order in the class Deltaproteobacteria. Then, based on polyphasic taxonomy analyses, a novel order Bradymonadales and a novel family Bradymonadaceae were proposed and validly published. Here, we reported the complete genome of this strain; the genome is 5,045,683 bp in size, has a GC content of 61.1% and contains 3992 predicted genes. Strain FA350T featured being able to prey on bacteria like the members from the order Myxococcales. This is in concordance with the fact that strain FA350T encoded genes affiliated with ABC-transporter, type IV pilus, type II secretion system, toxins and chemotaxis, which are known to play critical roles in bacterial predation. This genome data will provide insights into the bacterial predation pattern of strain FA350T and facilitate the investigation of the mutual interaction between predators and prey.Nucleotide sequence accession numberThe complete genome sequence of B. sediminis FA350T is available in the NCBI database (accession number CP030032). The strain has been deposited in the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Culture and China Centre of Industrial Culture Collection (=DSM 28820T = CICC 10904T).
  • De novo transcriptome assembly for Tracheliastes polycolpus, an invasive
           ectoparasite of freshwater fish in western Europe
    • Abstract: Publication date: Available online 7 January 2019Source: Marine GenomicsAuthor(s): Eglantine Mathieu-Bégné, Géraldine Loot, Simon Blanchet, Eve Toulza, Clémence Genthon, Olivier Rey Tracheliastes polycolpus is an ectoparasitic copepod that recently emerged in western Europe and that infects several freshwater fish species. Its recent successful spread might be due to its fascinating ability to shift to new host populations and/or species. Here, we present the first non-redundant and protein-coding de novo transcriptome assembly for T. polycolpus along with a quality assessment and reliable transcript annotations. This assembly was built from fifteen adult female parasites sampled from three different host species from a single river in southwestern France. Overall, 17,157 non-redundant contigs likely corresponding to protein-coding transcripts were identified, of which 13,093 (i.e., 76%) were successfully annotated. This assembly displayed good representativeness since 65.8% of the raw reads properly aligned back to the assembly. Similarly, 90.5% of the single copies of orthologues conserved across arthropods were retrieved in this assembly, which reflects a very good completeness. Finally, this transcriptome assembly gathered 7979 T. polycolpus specific transcripts when compared with the two closest referenced species (Lepeophtheirus salmonis and Caligus rogercresseyi), thus constituting an original genomic resource. This high-quality transcriptome is an important genomic resource for deciphering the molecular bases underlying host shifts in generalist parasites, and for studying the evolutionary biology of copepods that are major biological components of both freshwater and marine ecosystems.
  • Experimental infection with Anguillicola crassus alters immune gene
           expression in both spleen and head kidney of the European eel (Anguilla
    • Abstract: Publication date: Available online 5 January 2019Source: Marine GenomicsAuthor(s): Seraina E. Bracamonte, Paul R. Johnston, Klaus Knopf, Michael T. Monaghan Invasive parasites have been implicated in the declines of several freshwater species. The swim bladder nematode Anguillicola crassus was introduced into Europe in the 1980s and is considered a threat to the European eel (Anguilla anguilla). Infection affects stress resistance and swimming behaviour. European eels produce an immune response against the parasite during the late stages of infection and after repeated infections. We used RNA-seq to examine the molecular response to infection during the poorly understood early stage and identify expression of genes and associated processes that are modified in two immune organs of European eels 3 days post infection with A. crassus. In the spleen, 67 genes were differentially expressed, 32 of which were annotated. Most of these were involved in immune processes and their regulation. Other differentially expressed genes in the spleen were important for heme metabolism and heme turn-over. In the head kidney, 257 genes (134 annotated) were differentially expressed. Several of these were associated with immune functions. Other differentially expressed genes in the head kidney were related to renal function, in particular osmoregulation and paracellular flow. We conclude that the early response of European eels to A. crassus is complex and involves various processes aside from the immune system. We identified molecular changes occurring early during the infection and identified candidate genes and processes which will facilitate future studies aimed at determining the factors affecting European eel viability in the face of this invasive parasite.
  • Evidence of selective pressure in whale fall microbiome proteins and its
           potential application to industry
    • Abstract: Publication date: Available online 14 December 2018Source: Marine GenomicsAuthor(s): Robert Cardoso de Freitas, Helena Isabel Ferreira Marques, Marcus Adonai Castro da Silva, Angélica Cavalett, Estácio Jussie Odisi, Bianca Linhares da Silva, Jessica Engel Montemor, Takashi Toyofuku, Chiaki Kato, Katsunori Fujikura, Hiroshi Kitazato, André Oliveira de Souza Lima The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.
  • Complete genome of Pseudoalteromonas atlantica ECSMB14104, a
           Gammaproteobacterium inducing mussel settlement
    • Abstract: Publication date: Available online 4 December 2018Source: Marine GenomicsAuthor(s): Jin-Song Wang, Li-Hua Peng, Xing-Pan Guo, Asami Yoshida, Kiyoshi Osatomi, Yi-Feng Li, Jin-Long Yang, Xiao Liang Pseudoalteromonas is widely distributed in the marine environments and the biofilms formed by Pseudoalteromonas promote settlement of many species of invertebrates. Here, we show the complete genome of Pseudoalteromonas atlantica ECSMB14104, which was isolated from biofilms formed in the East China Sea and exhibited inducing activity on the Mytilus coruscus settlement. Complete genome of this strain containsa total of 3325 genes and the GC content of 41.02%. This genomic information is contributed to molecular mechanism of P. atlantica ECSMB14104 regulating mussel settlement.
  • Complete genome sequence of Pelolinea submarina MO-CFX1T within the phylum
           Chloroflexi, isolated from subseafloor sediment
    • Abstract: Publication date: Available online 22 November 2018Source: Marine GenomicsAuthor(s): Nozomi Nakahara, Yoshihiro Takaki, Miyuki Ogawara, Takashi Yamaguchi, Ken Takai, Hiroyuki Imachi Pelolinea submarina strain MO-CFX1T (=JCM 17238T, =KCTC 5975T) is an anaerobic chemoorganotrophic bacterium isolated from subseafloor sediments collected off the Shimokita Peninsula of Japan, north-western Pacific Ocean. This strain was the first isolate belonging to the phylum Chloroflexi from deep-sea sedimentary environment. Here, we report the complete genome sequence of this strain. This genome comprises 3,519,887 bp in a circular chromosome with GC content of 50.6% and contains 3131 protein-coding sequences. The genome contains a complete set of genes for the Embden–Meyerhof–Parnas pathway for glycolysis, coupled with its chemoorganotrophic growth ability with sugars. Similar to previously reported genomes of other members of the phylum Chloroflexi, the genome of this strain also lacks members of protein families associated with lipopolysaccharide production and diderm-specific outer membrane assembly, which are generally observed in typical Gram-negative bacterial cell envelopes. This finding suggests that the present strain possesses a monoderm cell envelope. The obtained genomic data provides insight into the physiological potential and the cell envelope characteristics of P. submarina strain MO-CFX1T and help to fill the gap in our knowledge about the phylum Chloroflexi.
  • An important resource for understanding bio-adhesion mechanisms: Cement
           gland transcriptomes of two goose barnacles, Pollicipes pollicipes and
           Lepas anatifera (Cirripedia, Thoracica)
    • Abstract: Publication date: Available online 16 November 2018Source: Marine GenomicsAuthor(s): André M. Machado, Elena Sarropoulou, L. Filipe C. Castro, Vitor Vasconcelos, Isabel Cunha Barnacles are sessile organisms globally distributed in marine and estuarine environments. The production of protein-based adhesives by cement glands is crucial for these organisms and plays a vital role in substrate attachment, thus inspiring biotechnological applications. Moreover, barnacles belong to bio-fouling communities, whose fixation onto man-made surfaces is of interest in terms of control and imposes an enormous economic cost on maritime industries. Here, we generated the first de novo assembly of cement gland transcriptomes of Pollicipes pollicipes (rocky-shore goose barnacle) and Lepas anatifera (pelagic goose barnacle) (Cirripedia, Thoracica), to generate molecular resources for understanding the bio-adhesion process in Cirripedia and to provide data for biotechnology. Via the Illumina next-generation sequencing technology, a total of 43.7 and 40.2 million (M) paired-end (PE) clean reads were obtained for P. pollicipes (PP) and L. anatifera (LA), respectively. De novo assemblies resulted in 116,377 transcripts for PP and 94,143 for LA, with N50 s of 1181 and 1028 bp, respectively. The Benchmarking Universal Single-Copy Orthologs (BUSCO) showed 78.7% (PP) and 91.7% (LA) of transcriptome completeness, in terms of expected gene content, for the Arthropoda phylum in each species. These results represent a substantial resource for expanding the knowledge on Cirripedia adhesion mechanisms and for contributions to the gene annotation of Crustacea where molecular resources are presently insufficient.
  • The complete genome sequence of the denitrifying bacterium Marinobacter
           sp. Arc7-DN-1 isolated from Arctic Ocean sediment
    • Abstract: Publication date: Available online 14 November 2018Source: Marine GenomicsAuthor(s): Yingying Meng, Zheng Zhang, Jiang Li, Yingtao Lv, Xuezheng Lin The general features and genome characteristics of the denitrifying bacterium Marinobacter sp. Arc7-DN-1, isolated from Arctic Ocean sediment, are described. Marinobacter sp. Arc7-DN-1 uses NO3− or NH4+ as the sole nitrogen source to grow at low temperatures. The strain can grow at a wide range of temperatures (0–30 °C) and NaCl concentration (15–90‰). The genome has one circular chromosome of 4,300,456 bp (57.64 mol% G + C content), consisting of 4012 coding genes, including 50 tRNAs and three rRNA operons as 16S-23S-5S rRNA. On the basis of the KEGG analysis, strain Arc7-DN-1 encodes 43 proteins related to nitrogen metabolism, including a complete denitrifying pathway and an assimilatory nitrate reduction pathway.
  • Population genomic footprints of environmental pollution pressure in
           natural populations of the Mediterranean mussel
    • Abstract: Publication date: Available online 14 November 2018Source: Marine GenomicsAuthor(s): Ângela M. Ribeiro, Carlos A. Canchaya, Fernando Penaloza, Juan Galindo, Rute R. da Fonseca Bivalve molluscs of the genus Mytilus are considered a model organism in ecotoxicology and are known to be well adapted to marine ecosystems affected by multiple anthropogenic factors, including pollution. In order to assess whether pollution interferes with the reproductive success of Mytilus and affects the diversity within and between populations, we sequenced the transcriptomes of 72 individuals from 9 populations of Mytilus galloprovincialis collected along a ca. 130-km north-south transect on the Western coast of the Iberian Peninsula. We found that polluted areas are acting as a barrier to gene flow, potentially because of the detrimental effect of anthropogenic chemicals on larvae carried from more pristine environments. Furthermore, we observed an increase in genetic diversity in populations from polluted site, which could be indicative of higher mutagenicity driven by the environment. We propose that a microevolutionary perspective is essential for a full characterization of human activities on the dispersal of M. galloprovincialis and that it should be incorporated into management, and conservation plans and policies in the context of the effects of pollution on populations.
  • Complete genome and data mining of Aeromicrobium sp. A1–2 isolated from
           the Southern Ocean
    • Abstract: Publication date: Available online 3 November 2018Source: Marine GenomicsAuthor(s): Li Liao, Shiyuan Su, Yong Yu, Jin Zhang, Bo Chen Aeromicrobium sp. A1–2, a putative new species isolated from marine sediments in the King George Island, Antarctica, was completely sequenced. The genome data showed biosynthetic potential of new natural products and clues for environmental adaptation of this actinobacterium.
  • The complete genome sequence of Thalassospira indica PB8BT insights into
           adaptation to the marine environment
    • Abstract: Publication date: Available online 26 October 2018Source: Marine GenomicsAuthor(s): Yang Liu, Qiliang Lai, Zongze Shao Thalassospira indica PB8BT was isolated from the deep water of the Indian Ocean. Here we report the complete genome sequence of type strain PB8BT, which comprises 4,701,725 bp with a G + C content of 54.9 mol%. We found that numerous genes related to iron acquisition, resistance, motility and chemotaxis, nitrogen, phosphorus and sulfur metabolism, and stress response. These metabolic features and related genes revealed genetic basis for the adaptation to the marine environment. The genome of T. indica PB8BT will be helpful for further insights into its adaptive evolution and ecological role in marine environment.
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