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  MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Levy Karin, E., Mirdita, M., & Söding, J. (2020). MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome, 8: 48. doi:10.1186/s40168-020-00808-x.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-CFF3-F Version Permalink: http://hdl.handle.net/21.11116/0000-0006-CFF8-A
Genre: Journal Article

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 Creators:
Levy Karin, E., Author
Mirdita, M.1, Author              
Söding, J.1, Author              
Affiliations:
1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              

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Free keywords: MetaEuk, Eukaryotes, Homology detection, Prediction, Annotation, Contigs, Marine
 Abstract: Background Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. Results MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk’s power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. Conclusion The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.

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Language(s): eng - English
 Dates: 2020-04-03
 Publication Status: Published online
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 Rev. Type: Peer
 Identifiers: DOI: 10.1186/s40168-020-00808-x
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Title: Microbiome
Source Genre: Journal
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Pages: 15 Volume / Issue: 8 Sequence Number: 48 Start / End Page: - Identifier: -