Subjects -> MATHEMATICS (Total: 1074 journals)
    - APPLIED MATHEMATICS (86 journals)
    - GEOMETRY AND TOPOLOGY (23 journals)
    - MATHEMATICS (793 journals)
    - MATHEMATICS (GENERAL) (43 journals)
    - NUMERICAL ANALYSIS (23 journals)
    - PROBABILITIES AND MATH STATISTICS (106 journals)

MATHEMATICS (793 journals)            First | 1 2 3 4     

Showing 401 - 538 of 538 Journals sorted alphabetically
Journal of Discrete Mathematics     Open Access   (Followers: 1)
Journal of Dynamics and Differential Equations     Hybrid Journal  
Journal of Engineering Mathematics     Hybrid Journal   (Followers: 2)
Journal of Evolution Equations     Hybrid Journal  
Journal of Experimental Algorithmics     Full-text available via subscription   (Followers: 1)
Journal of Flood Risk Management     Hybrid Journal   (Followers: 12)
Journal of Formalized Reasoning     Open Access   (Followers: 2)
Journal of Function Spaces     Open Access  
Journal of Functional Analysis     Full-text available via subscription   (Followers: 2)
Journal of Geochemical Exploration     Hybrid Journal   (Followers: 1)
Journal of Geological Research     Open Access   (Followers: 1)
Journal of Geovisualization and Spatial Analysis     Hybrid Journal  
Journal of Global Optimization     Hybrid Journal   (Followers: 6)
Journal of Global Research in Mathematical Archives     Open Access   (Followers: 1)
Journal of Group Theory     Hybrid Journal   (Followers: 2)
Journal of Homotopy and Related Structures     Hybrid Journal  
Journal of Honai Math     Open Access  
Journal of Humanistic Mathematics     Open Access   (Followers: 1)
Journal of Hyperbolic Differential Equations     Hybrid Journal  
Journal of Indian Council of Philosophical Research     Hybrid Journal  
Journal of Industrial Mathematics     Open Access   (Followers: 2)
Journal of Inequalities and Applications     Open Access  
Journal of Infrared, Millimeter and Terahertz Waves     Hybrid Journal   (Followers: 2)
Journal of Integrable Systems     Open Access   (Followers: 1)
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: 4)
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   (Followers: 1)
Journal of Numerical Cognition     Open Access  
Journal of Numerical Mathematics     Hybrid Journal   (Followers: 2)
Journal of Optimization     Open Access   (Followers: 4)
Journal of Peridynamics and Nonlocal Modeling     Hybrid Journal  
Journal of Problem Solving     Open Access   (Followers: 2)
Journal of Progressive Research in Mathematics     Open Access   (Followers: 1)
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   (Followers: 1)
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: 11)
Journal of Water and Land Development     Open Access   (Followers: 3)
JRAMathEdu : Journal of Research and Advances in Mathematics Education     Open Access   (Followers: 4)
JUMLAHKU : Jurnal Matematika Ilmiah STKIP Muhammadiyah Kuningan     Open Access   (Followers: 1)
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  
Lietuvos Matematikos Rinkinys     Open Access   (Followers: 1)
Limits : Journal of Mathematics and Its Applications     Open Access   (Followers: 1)
Linear Algebra and its Applications     Full-text available via subscription   (Followers: 23)
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: 4)
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 Forum Chitwan     Open Access   (Followers: 1)
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: 5)
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: 2)
Matrix Science Mathematic     Open Access   (Followers: 1)
Measurement Science Review     Open Access   (Followers: 3)
Mediterranean Journal of Mathematics     Hybrid Journal  
Memetic Computing     Hybrid Journal  
Mendel : Soft Computing Journal     Open Access  
Metaheuristics     Hybrid Journal  
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   (Followers: 1)
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: 7)
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)

  First | 1 2 3 4     

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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 - ISSN (Online) 1874-7787
Published by Elsevier Homepage  [3206 journals]
  • The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes
           and the question of sexual reproduction
    • Abstract: Publication date: Available online 11 February 2020Source: Marine GenomicsAuthor(s): Craig S. Wilding, Nicola Fletcher, Eleanor K. Smith, Peter Prentis, Gareth D. Weedall, Zac StewartAbstractThe beadlet anemone Actinia equina (L.) (Cnidaria: Anthozoa: Actiniaria: Actiniidae) is one of the most familiar organisms of the North European intertidal zone. Once considered a single, morphologically variable species across northern Europe, it is now recognised as one member of a variable species complex. Previous studies of distribution, aggression, allozymes and mitochondrial DNA suggest that the diversity in form and colour within A. equina may hide still unrecognised species diversity. To empower further study of A. equina population genetics and systematics, we sequenced (PacBio Sequel) the genome of a single A. equina individual to produce a high-quality genome assembly (contig N50 = 492,607 bp, 1485 contigs, number of protein coding genes = 47,671, 97% BUSCO completeness). There is debate as to whether A. equina reproduces solely asexually, since no reliable, consistent evidence of sexual reproduction has been found. To gain further insight, we examined the genome for evidence of a ‘meiotic toolkit’ – genes believed to be found consistently in sexually reproducing organisms – and demonstrate that the A. equina genome appears not to have this full complement. Additionally, Smudgeplot analysis, coupled with high haplotype diversity, indicates this genome assembly to be of ambiguous ploidy, suggesting that A. equina may not be diploid. The suggested polyploid nature of this species coupled with the deficiency in meiotic toolkit genes, indicates that further field and laboratory studies of this species is warranted to understand how this species reproduces and what role ploidy may play in speciation within this speciose genus.
       
  • The chloroplast genome sequence of the green macroalga Caulerpa okamurae
           (Ulvophyceae, Chlorophyta): Its structural features, organization and
           phylogenetic analysis
    • Abstract: Publication date: Available online 1 February 2020Source: Marine GenomicsAuthor(s): Fengrong Zheng, Bo Wang, Zhen Shen, Zongxing Wang, Wei Wang, Hongzhan Liu, Claire Wang, Maosheng XinAbstractTo clarify evolutionary characteristics, phylogenetic relationships as well as species identification of C. okamurae, we determined the cpDNA sequence of Caulerpa okamurae using de novo sequencing in the present study. The cpDNA of C. okamurae was 148,274 bp in length, and it lacked the inverted repeat commonly found in vascular green plants. The cpDNA of C. okamurae was highly compact with a gene density of 71.7%. Moreover, it was an AT-rich genome (65.5%) consisting 76 protein-coding genes (PCGs), 27 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 32 putative open reading frames (ORFs) and six introns. Additionally, the six introns were annotated in six genes as follows: psbA, rpoB, ftsH, psbD, atpF and cysA. The overall base composition of its cpDNA was 65.46% for AT. A total of 56 genes were encoded on the light strand, while all the other 50 chloroplast genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. Phylogenetic analyses suggested that the complete cpDNA sequence of C. okamurae fell in the Chlorophyta, Ulvophyceae, Bryopsidales, and Caulerpaceae and more resembled the cpDNAs of C. racemosa, C. cliftonii voucher and Tydemania expeditionis. Taken together, our data offered useful information for the studies of C.okamurae on evolutionary characteristics, phylogenetic relationships as well as species identification.
       
  • A comprehensive non-redundant reference transcriptome for the Atlantic
           silverside Menidia menidia
    • Abstract: Publication date: Available online 25 January 2020Source: Marine GenomicsAuthor(s): Nina Overgaard Therkildsen, Hannes BaumannAbstractThe Atlantic silverside (Menidia menidia) has been the focus of extensive research efforts in ecology, evolutionary biology, and physiology over the past three decades, but lack of genomic resources has so far hindered examination of the molecular basis underlying the remarkable patterns of phenotypic variation described in this species. We here present the first reference transcriptome for M. menidia. We sought to capture a single representative sequence from as many genes as possible by first using a combination of Trinity and the CLC Genomics Workbench to de novo assemble contigs based on RNA-seq data from multiple individuals, tissue types, and life stages. To reduce redundancy, we passed the combined raw assemblies through a stringent filtering pipeline based both on sequence similarity to related species and computational predictions of transcript quality, condensing an initial set of>480,000 contigs to a final set of 20,998 representative contigs, amounting to a total length of 53.3 Mb. In this final assembly, 91% of the contigs were functionally annotated with putative gene function and gene ontology (GO) terms and/or InterProScan identifiers. The assembly contains complete or nearly complete copies of>95% of 248 highly conserved core genes present in low copy number across higher eukaryotes, and partial copies of another 3.8%, suggesting that our assembly provides relatively comprehensive coverage of the M. menidia transcriptome. The assembly provided here will be an important resource for future research.
       
  • The genome of Ectocarpus subulatus – A highly
           stress-tolerant brown alga
    • Abstract: Publication date: Available online 11 January 2020Source: Marine GenomicsAuthor(s): Simon M. Dittami, Erwan Corre, Loraine Brillet-Guéguen, Agnieszka P. Lipinska, Noé Pontoizeau, Meziane Aite, Komlan Avia, Christophe Caron, Chung Hyun Cho, Jonas Collén, Alexandre Cormier, Ludovic Delage, Sylvie Doubleau, Clémence Frioux, Angélique Gobet, Irene González-Navarrete, Agnès Groisillier, Cécile Hervé, Didier Jollivet, Hetty KleinJanAbstractBrown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kützing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.
       
  • Genome of Alcanivorax sp. 24: A hydrocarbon degrading bacterium isolated
           from marine plastic debris
    • Abstract: Publication date: February 2020Source: Marine Genomics, Volume 49Author(s): V. Zadjelovic, M.I. Gibson, C. Dorador, J.A. Christie-OlezaAbstractAlcanivorax 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: February 2020Source: Marine Genomics, Volume 49Author(s): Erica Mendes Lopes, Camila Cesário Fernandes, Eliana G. de Macedo Lemos, Luciano Takeshi KishiAbstractMarinobacter 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.
       
  • Microbial communities associated with the parasitic copepod
           Lepeophtheirus salmonis
    • Abstract: Publication date: February 2020Source: Marine Genomics, Volume 49Author(s): S. Dalvin, K.O. Skaftnesmo, K. Malde, K.A. Glover, J.S. Leong, B.F. Koop, R.B. Edvardsen, N. SandlundAbstractLepeophtheirus 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.
       
  • The isolation and genome sequencing of a novel cyanophage S-H68 from the
           Bohai Sea, China
    • Abstract: Publication date: Available online 2 January 2020Source: Marine GenomicsAuthor(s): Chenglong Xue, Xinxin Liu, Qi Wang, Tongtong Lin, Min Wang, Qian Liu, Hongbing Shao, Yong JiangAbstractCyanobacteria, also known as bule-green algae, are capable of photosynthesis and have a fixed carbon and nitrogen effect. The virus that specifically infects cyanobacteria is called the cyanophage. Cyanophages play a key role in building microbial communities. However, only a small number of cyanophages have been reported so far. In this study, a novel Synechococcus cyanophage S-H68 was isolated from the Bohai Sea of China. Transmission electron microscope observations showed that S-H68 has an icosahedral head, 66 ± 1 nm in diameter, and a tail with a length of 107 ± 1 nm, and should be grouped into the family Siphoviridae. To better understand the genetic diversity of this cyanophage, the complete genome was characterized. It consists of 79,639 –bp –length double-stranded DNA with a GC content of 59.8% and is predicted to have 117 open reading frames (ORFs) with an average length of 655 nucleotides. Using the BLASTN tool in the NCBI database for genome comparison, there was no significant similarity between S-H68 and other known cyanophages. So the present study added a new Siphoviridae cyanophage to the marine phage dataset.
       
  • Cytogenetic characterization of the Antarctic silverfish Pleuragramma
           antarctica (Boulenger 1902) through analysis of mitotic chromosomes from
           early larvae
    • Abstract: Publication date: Available online 28 December 2019Source: Marine GenomicsAuthor(s): Laura Ghigliotti, Chi-Hing C. Cheng, Catherine Ozouf-Costaz, Chantal Guidi-Rontani, Marino Vacchi, Sara Federici, Eva PisanoAbstractThis paper describes the cytogenetic features of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902), a keystone species of the Antarctic coastal marine ecosystem. Conventional cytogenetic analyses and physical mapping of repetitive DNA sequences were performed on metaphase plates obtained through direct chromosome preparation from P. antarctica early larvae.The Antarctic silverfish have a diploid number (2n) = 48, and a karyotype made up of a majority of two-armed chromosomes (karyotype formula36m/sm + 10st + 2a, fundamental number = 94). Major ribosomal gene repeats were detected on three chromosome pairs (20, 21, and 23), in correspondence of dim DAPI stained regions. Long Interspersed Nuclear Elements (LINEs) were abundant and wide spread over all chromosomes.Overall, the cytogenetic data presented herein are consistent with a long independent cytogenetic and evolutionary history for the species. The large number of two-armed chromosomes, indicative of highly-rearranged karyotype, coupled with a diploid number of 48, a presumed primitive character for this fish group, and the spread of the major ribosomal genes on three chromosome pairs, make the Antarctic silverfish distinct from all other notothenioid species.
       
  • Short communication: Characterization of the expression of microRNAs in
           the poecilogonous polychaete B. wellingtonensis
    • Abstract: Publication date: Available online 26 December 2019Source: Marine GenomicsAuthor(s): Alvaro Figueroa, Leyla Cárdenas, Martin Caicedo, Fernanda X. Oyarzun, Daniel Doherty-Weason, Antonio BranteAbstractPoecilogony is a type of reproduction in which a species produces different types of larvae. Boccardia wellingtonensis, is a poecilogonous polychaete with females producing planktotrophic and adelphophagic larvae, in addition to nurse eggs, in the same capsule that differ in feeding behavior. It is still unclear why planktotrophs do not feed on nurse eggs during the intracapsular development and arrest its growth, while adelphophagic larvae consume nurse eggs and planktotrophic larvae inside the capsule, hatching as advance larvae or as juveniles. Here we characterized the expression of selected miRNAs from these two types of larvae and from adults in order to begin to understand the molecular mechanisms that regulate expression in this type of poecilogony. Results showed that adults and pre-hatching adelphophagic larvae have high levels of expression of miR-125, miR-87a and let-7, while adelphophages at early developmental stage had low levels of expression of miR-87b. Planktotrophic larvae showed low expression level of let-7. This work represents the first step in understanding the role of miRNAs in the development of different larval types in a poecilogonous species. We also propose to B. wellingtonensis as an interesting biological model to study the evolution of larval modes and reproductive strategies of marine invertebrates.
       
  • Microscopic ossicle analyses and the complete mitochondrial genome
           sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea)
           provide new information to support the phylogenetic positioning of this
           sea cucumber species
    • Abstract: Publication date: Available online 19 December 2019Source: Marine GenomicsAuthor(s): Valerio Joe Utzeri, Anisa Ribani, Samuele Bovo, Valeria Taurisano, Matteo Calassanzio, David Baldo, Luca FontanesiSea cucumbers (Holothuroidea) are ecologically important organisms for their bioturbation and alkalinization activities of the seabed. These species are extensively fished as they are considered luxury food. Sea cucumbers are also relevant for biomedical studies and the production of bioactive compounds. A few initiatives are recently evaluating sea cucumbers as novel aquaculture species. The aim of this study was to provide morphological and genetic information useful for the identification of Holothuria polii, the white spot sea cucumber (a common species of the Mediterranean Sea). We generated the complete sequence of the mitochondrial DNA (mtDNA) genome of this species and combined it with a detailed ossicle characterization of the sequenced specimen by scanning electron microscopic analysis. Ossicles (known also as sclerites) are anatomical features that can discriminate Holothuroidea species, including the closely related ones of the genus Holothuria. The complete mitochondrial genome was assembled, functionally annotated and then used to evaluate the phylogenetic relationship of H. polii against the other few Holothuroidea species for which the whole mtDNA was available. The 15,907 bp H. polii mtDNA sequence has the same gene order already reported for H. scabra, H. forskali and other species of the same class. Cox1 and 16S gene sequences were informative for species identification across the genus and could be used for the authentication of commercialized Holothuria spp. The mitochondrial genome sequence presented here provides the basis to a future analysis of the variability of H. polii populations in the Mediterranean region.Graphical abstractUnlabelled Image
       
  • De novo transcriptome assembly of the Qatari pearl oyster Pinctada
           imbricata radiata
    • Abstract: Publication date: Available online 7 December 2019Source: Marine GenomicsAuthor(s): Tim P. Bean, Zenaba Khatir, Brett P. Lyons, Ronny van Aerle, Diana Minardi, John P. Bignell, David Smyth, Bruno Welter Giraldes, Alexandra LeitãoAbstractThe pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and the species is now under threat due to multiple confounding pressures. This manuscript presents the first de novo transcriptome of the Qatari pearl oyster assembled into 30,739 non-redundant coding sequences and with a BUSCO completeness score of 98.4%. Analysis of the transcriptome reveals the close evolutionary distance to the conspecific animal Pinctada imbricata fucata but also highlights differences in immune genes and the presence of distinctive transposon families, suggesting recent adaptive divergence. This data is made available for all to utilise in future studies on the species.
       
  • Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic
           marine bacterium isolated from a deep-sea hydrothermal vent on the
           Southwest Indian Ridge
    • Abstract: Publication date: Available online 27 November 2019Source: Marine GenomicsAuthor(s): Xue-Gong Li, Wei-Jia Zhang, Xiao-Qing Qi, Long-Fei WuAbstractCrassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes, and 34 rRNA genes. Numerous genes are related to peptide transport, amino acid metabolism, motility, and sporulation. This agrees with the observation that strain SY095 is a spore-forming, motile, and chemoheterotrophic bacterium. Further, the genome harbors multiple prophages that carry all the genes necessary for viral particle synthesis. Some prophages carry additional genes that may be involved in the regulation of sporulation. This is the first reported genome of a bacterium from the genus Crassaminicella, providing insights into the microbial adaptation strategies to the deep-sea hydrothermal vent environment.
       
  • t-Distributed Stochastic Neighbor Embedding (t-SNE): A tool for
           eco-physiological transcriptomic analysis
    • Abstract: Publication date: Available online 26 November 2019Source: Marine GenomicsAuthor(s): Matthew C. Cieslak, Ann M. Castelfranco, Vittoria Roncalli, Petra H. Lenz, Daniel K. HartlineAbstractHigh-throughput RNA sequencing (RNA-Seq) has transformed the ecophysiological assessment of individual plankton species and communities. However, the technology generates complex data consisting of millions of short-read sequences that can be difficult to analyze and interpret. New bioinformatics workflows are needed to guide experimentation, environmental sampling, and to develop and test hypotheses. One complexity-reducing tool that has been used successfully in other fields is “t-distributed Stochastic Neighbor Embedding” (t-SNE). Its application to transcriptomic data from marine pelagic and benthic systems has yet to be explored. The present study demonstrates an application for evaluating RNA-Seq data using previously published, conventionally analyzed studies on the copepods Calanus finmarchicus and Neocalanus flemingeri. In one application, gene expression profiles were compared among different developmental stages. In another, they were compared among experimental conditions. In a third, they were compared among environmental samples from different locations. The profile categories identified by t-SNE were validated by reference to published results using differential gene expression and Gene Ontology (GO) analyses. The analyses demonstrate how individual samples can be evaluated for differences in global gene expression, as well as differences in expression related to specific biological processes, such as lipid metabolism and responses to stress. As RNA-Seq data from plankton species and communities become more common, t-SNE analysis should provide a powerful tool for determining trends and classifying samples into groups with similar transcriptional physiology, independent of collection site or time.
       
  • De novo transcriptome sequencing of the thecate colonial hydrozoan,
           Dynamena pumila
    • Abstract: Publication date: Available online 24 November 2019Source: Marine GenomicsAuthor(s): Daria Kupaeva, Evgenii Konorov, Stanislav KremnyovAs the sister group to bilaterian animals, cnidarians are very valuable models for comparative transcriptomics, shedding light on the evolution and genetic regulation of developmental trajectories, morphogenesis, body patterning and regeneration. To gain deeper insights into the evolution of developmental processes, wider sampling of biological diversity should be performed. In this study, we report the sequencing, assembly and analysis of the transcriptome for the first sertulariid hydrozoan, Dynamena pumila. We sequenced a mixed cDNA library from several developmental stages using Illumina HiSeq 4000. These sequences were assembled into 76,196 contigs with an N50 of 1890 bp. The pool of assembled sequences represents a wide variety of genes expressed during Dynamena development. Functional annotation with Gene Ontology and KEGG pathway analysis has been performed. With this, we identified Dynamena transcripts corresponding to the genes involved in major developmental signalling pathways, including Wnt and TGF-β. The data obtained contribute to the further development of evolutionary and functional transcriptomics and provide the reference transcriptome for future studies.Graphical abstractUnlabelled Image
       
  • The first reference transcriptome assembly of the stalked barnacle,
           Neolepas marisindica, from the Onnuri Vent Field on the Central Indian
           Ridge
    • Abstract: Publication date: December 2019Source: Marine Genomics, Volume 48Author(s): Taewoo Ryu, Seonock Woo, Nayoung LeeAbstractNeolepas 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: December 2019Source: Marine Genomics, Volume 48Author(s): Taewoo Ryu, In-Young Cho, Sung-Jin Hwang, Seungshic Yum, Min-Seop Kim, Seonock WooAbstractEleutherobia 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.
       
  • Microarray analysis of gene expression of Atlantic cod from different
           Baltic Sea regions: Adaptation to salinity
    • Abstract: Publication date: December 2019Source: Marine Genomics, Volume 48Author(s): Magdalena Malachowicz, Roman WenneAbstractThe 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.
       
  • Complete genome sequence of Pseudoalteromonas sp. MEBiC 03485, isolated
           from deep-sea sediment
    • Abstract: Publication date: December 2019Source: Marine Genomics, Volume 48Author(s): Min Seo Jeon, Jeong-Joo Oh, Sang-Il Han, Chulhwan Park, Changsu Lee, Yoon-E ChoiAbstractPseudoalteromonas 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.
       
  • Looking for the hidden: Characterization of lysogenic phages in potential
           pathogenic Vibrio species from the North Sea
    • Abstract: Publication date: Available online 19 November 2019Source: Marine GenomicsAuthor(s): Alexa Garin-Fernandez, Antje WichelsAbstractThe incidence of potentially pathogenic Vibrio species in the marine environment around Europe, is correlated with the increase of surface seawater temperature. Despite their importance, little is known about the trigger factors of potential outbreak-causing strains in this region. As prophages may compose a major reservoir of virulence traits in marine ecosystems, this study aims to identify and characterize the genomes of lysogenic Vibrio phages exemplarily from the North Sea. Therefore, 31 isolates from potentially pathogenic Vibrio species from the North Sea were screened for inducible prophages with mitomycin C. From them, one V. cholerae isolate and 40% V. parahaemolyticus isolates carried inducible prophages. Three lysogenic phages were selected for genomic characterization. The phage vB_VpaM_VP-3212 (unclassified Myoviridae) has a genome with a length of 36.81 Kbp and 55 CDS were identified. This lysogenic phage of V. parahaemolyticus contains genes related to replicative transposition mechanism, such as transposase and mobile elements similar to Mu-like viruses. The phage vB_VpaP_VP-3220 (Podoviridae, unclassified Nona33virus) has a genome length of 58,14 Kbp and contains 63 CDS. This V. parahaemolyticus phage probably uses a headful (pac) packaging replication mechanism. The phage vB_VchM_VP-3213 (unclassified Myoviridae) has a genome with a length of 41 Kbp and 63 CDS were identified, including integrase and Xer system for lysogenic recombination. This lysogenic phage of V. cholerae has similar genomic features as lambdoid phages. Although no pathogenicity genes were identified, their similarity among other phage genomes indicates that these phages can affect the development of pathogenic Vibrio strains in marine environments.
       
  • Adaptations to environmental change: Globin superfamily evolution in
           Antarctic fishes
    • Abstract: Publication date: Available online 14 November 2019Source: Marine GenomicsAuthor(s): Jacob M. Daane, Daniela Giordano, Daniela Coppola, Guido di Prisco, H. William Detrich, Cinzia VerdeAbstractThe ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic notothenioids, emphasizing their adaptive features as inferred from comparisons with human proteins.We dedicate this review to Guido di Prisco, our co-author, colleague, friend, and husband of C.V. Ever thoughtful, creative, and enthusiastic, Guido spearheaded study of the structure, function, and evolution of the hemoglobins of polar fishes – this review is testimony to his wide-ranging contributions. Throughout his career, Guido inspired younger scientists to embrace polar biological research, and he challenged researchers of all ages to explore evolutionary adaptation in the context of global climate change. Beyond his scientific contributions, we will miss his warmth, his culture, and his great intellect. Guido has left an outstanding legacy, one that will continue to inspire us and our research.
       
  • Globins and nitric oxide homeostasis in fish embryonic development
    • Abstract: Publication date: Available online 8 November 2019Source: Marine GenomicsAuthor(s): Elizabeth R. Rochon, Paola CortiAbstractSince the discovery of new members of the globin superfamily such as Cytoglobin, Neuroglobin and Globin X, in addition to the most well-known members, Hemoglobin and Myoglobin, different hypotheses have been suggested about their function in vertebrates. Globins are ubiquitously found in living organisms and can carry out different functions based on their ability to bind ligands such as O2, and nitric oxide (NO) and to catalyze reactions scavenging NO or generating NO by reducing nitrite. NO is a highly diffusible molecule with a central role in signaling important for egg maturation, fertilization and early embryonic development. The globins ability to scavenge or generate NO makes these proteins ideal candidates in regulating NO homeostasis depending on the micro environment and tissue NO demands. Different amounts of various globins have been found in zebrafish eggs and developing embryos where it's unlikely that they function as respiratory proteins and instead could play a role in maintaining embryonic NO homeostasis. Here we summarize the current knowledge concerning the role of NO in adult fish in comparison to mammals and we discuss NO function during embryonic development with possible implications for globins in maintaining embryonic NO homeostasis.
       
  • Complete genome sequence of Dyadobacter sp. 32, isolated from a culture of
           the freshwater diatom Cymbella microcephala
    • Abstract: Publication date: Available online 5 November 2019Source: Marine GenomicsAuthor(s): Lachlan Dow, Kathryn Lee Morrissey, Anne Willems, Peter G. KrothAbstractBacteria have been shown to be involved in different species-specific interactions with eukaryotic algae such as diatoms, impacting important ecosystem processes. Recently, a strain assigned to Dyadobacter, named ‘species 32’, has been shown to be involved in a number of ecologically relevant diatom processes, such as biofilm formation or growth enhancement, depending on the diatom species. This bacterium was originally isolated from a culture of freshwater benthic diatoms that originated from an epilithic biofilm, in which both bacteria and diatoms coexist. A single complete circular chromosome of Dyadobacter sp. 32 was assembled with a length of 7,101,228 bp, containing 6062 protein coding genes and 3 rRNA operons. A number of interesting genetic features were found, such as a putative zeaxanthin biosynthetic gene cluster. A large number of polysaccharide utilizing gene clusters were also detected, along with genes potentially acquired from other bacteria through horizontal gene transfer, and genes previously identified in other algae-bacteria interactions. These data serve to increase our understanding of specific interactions within freshwater biofilms, and identify a number of gene targets with which to study the molecular basis of diatom-bacteria interactions.
       
  • Complete genome sequence of Echinicola rosea JL3085, a xylan and
           pectin decomposer
    • Abstract: Publication date: Available online 31 October 2019Source: Marine GenomicsAuthor(s): Peiwen Zhan, Jianing Ye, Xiaopei Lin, Fan Zhang, Dan Lin, Yao Zhang, Kai TangAbstractMarine Bacteroidetes are well known for their functional specialization on the decomposition of polysaccharides which results from a great number of carbohydrate-active enzymes. Here we represent the complete genome of a Bacteroitedes member Echinicola rosea JL3085T that was isolated from surface seawater of the South China Sea. The genome is 6.06 Mbp in size with a GC content of 44.1% and comprises 4613 protein coding genes. A remarkable genomic feature is that the number of glycoside hydrolase genes in the genome of E. rosea JL3085T is high in comparison with most of the sequenced members of marine Bacteroitedes. E. rosea JL3085T genome harbored multi-gene polysaccharide utilization loci (PUL) systems involved in the degradation of pectin, xylan and arabinogalactan. The large diversity of hydrolytic enzymes supports the use of E. rosea JL3085T as a candidate for biotechnological applications in enzymatic conversion of plant polysaccharides.
       
  • Complete genome sequence of Acinetobacter baumanni J1, a quorum
           sensing-producing algicidal bacterium, isolated from Eastern Pacific Ocean
           
    • Abstract: Publication date: Available online 31 October 2019Source: Marine GenomicsAuthor(s): Chen Zhang, Yao Li, Chen-Xu Meng, Ming-Jun Yang, Yong-Gang Wang, Zhong-Hua Cai, Ping Zuo, Jin ZhouAbstractThe Acinetobacter baumanni J1 isolated from surface water of the Eastern Pacific Ocean, demonstrated significant algicidal activity on the algae Alexandrium tamarense. Interestingly, this strain showed the ability to produce an acyl-homoserine lactone (AHL) quorum sensing molecule. To better understand its AHL producing mechanism and its ecological functions, the genome of A. baumanni strain J1 was completely sequenced. The genome contained a circular chromosome of 3,948,465 bp with an average GC content of 39.9 mol%. A total of 3707 protein coding genes, 41 tRNA genes and 16 rRNA genes were obtained. In silico genome annotation identified a LuxI putative gene located on contig 4. Subsequent thin-layer chromatography analysis indicated that C8-AHL could be produced by A. baumanni J1, which confirmed the authenticity of the LuxI gene. Taken together, this work describes an algicidal bacterium that is capable of producing an AHL molecule, which may represent a valuable tool for developing microbial methods to control harmful algae.
       
  • Environmental regulation of the function of circulating erythrocytes via
           changes in age distribution in teleost fish: Possible mechanisms and
           significance
    • Abstract: Publication date: Available online 31 October 2019Source: Marine GenomicsAuthor(s): Mikko NikinmaaAbstractThe blood of fish has a continuous age distribution of erythrocytes. The properties of young and old erythrocytes differ with young erythrocytes being functionally much more versatile than old erythrocytes, which have higher haemoglobin content. Factors which affect the formation and breakdown of erythrocytes are reviewed. Erythropoiesis in fish is largely similar to that in mammals. However, definitive erythrocytes are mainly formed in the anterior part of the kidney, and erythropoietin is secreted mainly from the heart. Senescence of erythrocytes in fish has not been studied in detail, and consecutively the factors causing aging of erythrocytes in man are discussed. A major factor causing aging of erythrocytes is oxidative stress, which is also a major effect of toxicants on fish erythrocytes. Consequently, apparent age distribution of circulating erythrocytes will be affected by environmental pollution. At present, it is completely unknown, if the changes in age distribution of erythrocytes play a role in pollutant responses or if the age distribution of erythrocytes is actively regulated during environmental adaptation.
       
  • Complete genome sequence of the novel alginolytic Psychroserpens sp.
           NJDZ02 isolated from macroalgae collected from King George Island,
           Antarctica
    • Abstract: Publication date: Available online 13 September 2019Source: Marine GenomicsAuthor(s): Xiaoqian Gu, Jiang Li, Xuezheng Lin, Yuanyuan Gui, Aihong PanAbstractThe 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 MoragaAbstractIn 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
           fish
    • Abstract: Publication date: Available online 30 August 2019Source: Marine GenomicsAuthor(s): Albina Kochneva, Polina Drozdova, Ekaterina BorvinskayaAbstractThe 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. WilsonAbstractThe 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. TibbitsAbstractThe 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 StuckasAbstractMytilus 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 ShaoAbstractMarinobacter 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. PlaceAbstractDespite 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 ShinAbstractAntarcticibacterium 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 NakaiAbstractTo 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 LinAbstractParacoccus 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 WangAbstractMarinimicrobia 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
           development
    • Abstract: Publication date: Available online 19 June 2019Source: Marine GenomicsAuthor(s): Juliet M. Wong, Juan D. Gaitán-Espitia, Gretchen E. HofmannAbstractThe 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 WangAbstractTwo 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 JørgensenAbstractDesulfobacter 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 ZhangAbstractA 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 QuAbstractThe 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.
       
  • 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. EdwardsAbstractBackgroundHigh-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.
       
  • 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 YangAbstractVibrio 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 ChenAbstractJanibacter 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.
       
 
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