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

View ORCID ProfileEli Levy Karin, View ORCID ProfileMilot Mirdita, View ORCID ProfileJohannes Söding
doi: https://doi.org/10.1101/851964
Eli Levy Karin
1Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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  • ORCID record for Eli Levy Karin
  • For correspondence: eli.levy.karin@gmail.com soeding@mpibpc.mpg.de
Milot Mirdita
1Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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Johannes Söding
1Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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  • For correspondence: eli.levy.karin@gmail.com soeding@mpibpc.mpg.de
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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 eight 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.

Footnotes

  • https://github.com/soedinglab/metaeuk

  • http://wwwuser.gwdg.de/~compbiol/metaeuk/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 25, 2019.
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MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Eli Levy Karin, Milot Mirdita, Johannes Söding
bioRxiv 851964; doi: https://doi.org/10.1101/851964
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MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Eli Levy Karin, Milot Mirdita, Johannes Söding
bioRxiv 851964; doi: https://doi.org/10.1101/851964

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