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Journal Cover Metabarcoding and Metagenomics
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  This is an Open Access Journal Open Access journal
   ISSN (Online) 2534-9708
   Published by Pensoft Homepage  [25 journals]
  • Disentangling higher trophic level interactions in the cabbage aphid food
           web using high-throughput DNA sequencing

    • Abstract: Metabarcoding and Metagenomics 1: e13709
      DOI : 10.3897/mbmg.1.13709
      Authors : Marie-Caroline Lefort, Stephen Wratten, Antonino Cusumano, Yann-David Varennes, Stephane Boyer : The lack of understanding of complex food-web interactions has been a major gap in the history of biological control. In particular, a better understanding of the functioning of pest food-webs and how they vary between native and invaded geographical ranges is of prime interest for biological control research and associated integrated pest management. Technical limitations associated with the deciphering of complex food-webs can now be largely overcome by the use of high throughput DNA sequencing techniques such as Illumina MiSeq. We tested the efficiency of this next generation sequencing technology in a metabarcoding approach, to study aphid food-webs using the cabbage aphid as model. We compared the variations in structure and composition of aphid food-webs in the species’ native range (United Kingdom, UK) and in an invaded range (New Zealand, NZ). We showed that Illumina MiSeq is a well suited technology to study complex aphid food-webs from aphid mummies. We found an unexpectedly high top down pressure in the NZ cabbage aphid food-web, which coupled to a large ratio of consumer species / prey species and a lack of potential inter-specific competition between primary parasitoids, could cause the NZ food-web to be more vulnerable than the UK one. This study also reports for the first time the occurrence of a new hyperparasitoid species in NZ, as well as new associations between hyperparasitoids parasitoids and the cabbage aphid in this country. We conclude that the complexity of aphid food-webs in agricultural systems could often be underestimated, particularly at higher trophic levels; and that the use of high throughput DNA sequencing tools, could largely help to overcome this impediment. HTML XML PDF
      PubDate: Wed, 18 Oct 2017 14:38:41 +030
       
  • Ready for the deluge! Introducing the new Metabarcoding and Metagenomics
           (MBMG) journal

    • Abstract: Metabarcoding and Metagenomics 1: e14791
      DOI : 10.3897/mbmg.1.14791
      Authors : Florian Leese, Dirk Steinke, Alexander Weigand, Lyubomir Penev : HTML XML PDF
      PubDate: Wed, 20 Sep 2017 15:15:10 +030
       
  • Short COI markers for freshwater macroinvertebrate metabarcoding

    • Abstract: Metabarcoding and Metagenomics 1: e14625
      DOI : 10.3897/mbmg.1.14625
      Authors : Ecaterina Vamos, Vasco Elbrecht, Florian Leese : Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental DNA (eDNA) filtered from water or gut content analyses. Here universal primer sets targeting only a short COI fragment are advantageous, as they often can still amplify short DNA fragments. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vitro by sequencing previously used freshwater macroinvertebrate mock communities as well as three monitoring samples from Romanian streams of unknown composition. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vitro, detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2+BR2) revealed that detection efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest. HTML XML PDF
      PubDate: Wed, 20 Sep 2017 10:33:01 +030
       
  • Functional and phylogenetic analysis of the core transcriptome of
           Ochromonadales

    • Abstract: Metabarcoding and Metagenomics 1: e19862
      DOI : 10.3897/mbmg.1.19862
      Authors : Nadine Graupner, Jens Boenigk, Christina Bock, Manfred Jensen, Sabina Marks, Sven Rahmann, Daniela Beisser : Background Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model group to study the core genes and metabolic pathways of a functionally diverse lineage. The objective of our study is the identification of the joint genetic repertoire expressed in closely related chrysophytes as well as the extent of variation on species and strain level. Therefore, we investigated the transcriptomes of six strains belonging to four species of Ochromonadales. We performed analyses on metabolic pathway level as well as on sequence level. Results We could identify 1,574 core genes shared between all six investigated strains of Ochromonadales. Most of these core genes were affiliated with the primary metabolism. Phylogenetic analysis of 166 protein-coding core genes supported a close relation of Poteriospumella lacustris and Poterioochromonas malhamensis and resolved for more than 50% of investigated genes the relationship of strains affiliated with the species P. lacustris. Further, we found diverging phylogenetic patterns for genes interacting with the environment. Conclusions In Ochromonadales, a functionally diverse lineage, the core transcriptome represents only a minor part of the individual transcriptomes. But this small fraction of genes comprises the basal metabolism essential for life in several protist lineages. Phylogenetic analyses of these genes indicate a similar degree of conservation as observed for genes coding for ribosomal proteins. HTML XML PDF
      PubDate: Wed, 20 Sep 2017 9:13:36 +0300
       
 
 
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