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 samples. We investigated the co-abundance patterns of ~37 million 44 eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions 45 to assess the diversity and functional profiles of marine plankton. We identified ~12 thousand co-46 abundant gene groups (CAGs), encompassing ~7 million unigenes, including 924 metagenomics 47 the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing 53 haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource 54for an exhaustive analysis of eukaryotic plankton in the open ocean by giving access to the genomic 55 content and functional potential of many ecologically relevant eukaryotic species. 56

Unifying the known and unknown microbial coding sequence space

“…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.…”

DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications

“…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).…”

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

“…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 ).…”

“…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.…”