2019
DOI: 10.1101/812974
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Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics

Abstract: 38Large scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-39 centric approach, limiting the ability to understand organismal and community biology. De novo 40 assembly of large and mosaic eukaryotic genomes from complex meta -omics data remains a 41 challenging task, especially in comparison with more straightforward bacterial and archaeal 42 systems. Here we use a transcriptome reconstruction method based on clustering co-abundant genes 43 across a series of metagenomic… Show more

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Cited by 10 publications
(13 citation statements)
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“…The results presented here prove that the integration and the analysis of the unknown fraction are possible. We are unveiling a brighter future, not only for microbiome analyses but also for boosting eukaryotic-related studies, thanks to the increasing number of projects, including metatranscriptomic data (Delmont et al, 2020;Vorobev et al, 2020). Furthermore, our work lays the foundations for further developments of clear guidelines and protocols to define the different levels of unknown (Thomas & Segata, 2019) and should encourage the scientific community for a collaborative effort to tackle this challenge.…”
Section: Discussionmentioning
confidence: 97%
“…The results presented here prove that the integration and the analysis of the unknown fraction are possible. We are unveiling a brighter future, not only for microbiome analyses but also for boosting eukaryotic-related studies, thanks to the increasing number of projects, including metatranscriptomic data (Delmont et al, 2020;Vorobev et al, 2020). Furthermore, our work lays the foundations for further developments of clear guidelines and protocols to define the different levels of unknown (Thomas & Segata, 2019) and should encourage the scientific community for a collaborative effort to tackle this challenge.…”
Section: Discussionmentioning
confidence: 97%
“…EukRep (West et al, 2018) is a reference-independent application that uses k-mer frequency and linear-SVM to classify metagenomic contigs into eukaryotic and prokaryotic sequences. It has been proven that when combined with the conventional metagenomic and metatranscriptomic analyses, such as reconstructing eukaryotic bins and gene co-abundance analysis, biological and ecological insight can be readily obtained for uncultured eukaryotes (Vorobev et al, 2020;West et al, 2018).…”
Section: Introductionmentioning
confidence: 99%
“…The Tara Oceans imaging dataset 30 is also underutilized, especially due to the lack of well-established workflows. Overall, the cyanobacterial diazotrophs, especially those with diverse lifestyles (colonial, symbiotic, chain formers), have been poorly characterized (with the exception of UCYN-A 11, 16, 22, 26, 28, 31 ).…”
Section: Introductionmentioning
confidence: 99%
“…However, the larger plankton size fractions (>0.8 µm) enriched in eukaryotes are genomically much more complex, and thus current Tara Oceans gene catalogs from these fractions are based only on poly-A-tailed eukaryotic RNA 24,25 . Hence, the prokaryotes from these larger size fractions have been unstudied and are limited to specific taxa based on these poly-A assembled sequences [26][27][28] , whose signal is difficult to interpret quantitatively 29 . The Tara Oceans imaging dataset 30 is also underutilized, especially due to the lack of well-established workflows.…”
Section: Introductionmentioning
confidence: 99%