ArticleGenome research2020
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 83 citations in OpenAlex.
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.Nucleic acids research · 2026Article
- Article
- Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?Molecular ecology · 2025Article
- Insights into putative alginate lyases from epipelagic and mesopelagic communities of the global ocean.Scientific reports · 2025Article
- DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.NAR genomics and bioinformatics · 2024Article
- DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms.Nature microbiology · 2023Article
- Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations.BMC ecology and evolution · 2023Article
- Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.Microbiome · 2023Article
- A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.Molecular biology and evolution · 2023Article
- Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly.BMC bioinformatics · 2023Article
- Environmental DNA sequencing reveals the regional difference in diversity and community assembly mechanisms of eukaryotic plankton in coastal waters.Frontiers in microbiology · 2023Article
- Primer design for the amplification of the ammonium transporter genes from the uncultured haptophyte algal species symbiotic with the marine nitrogen-fixing cyanobacterium UCYN-A1.Frontiers in microbiology · 2023Article
- Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea.Environmental microbiology · 2022Article
- Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomics datasets.Molecular ecology resources · 2022Article
- SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data.NAR genomics and bioinformatics · 2022Article
- The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.Nucleic acids research · 2022Article
- Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.Cell genomics · 2022Article
- Article
- Towards omics-based predictions of planktonic functional composition from environmental data.Nature communications · 2021Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ∼37 million eukaryotic unigenes across 365 metagenomic samples collected during the
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.