Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns.

Autor: Le AV; Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic., Větrovský T; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic., Barucic D; Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic., Saraiva JP; Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany., Dobbler PT; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic., Kohout P; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic., Pospíšek M; Department of Genetics and Microbiology, Charles University, Praha, Czech Republic., da Rocha UN; Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany., Kléma J; Department of Computer Science, Czech Technical University in Prague, Praha, Czech Republic., Baldrian P; Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2023 Nov; Vol. 23 (8), pp. 1800-1811. Date of Electronic Publication: 2023 Aug 10.
DOI: 10.1111/1755-0998.13852
Abstrakt: Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.
(© 2023 John Wiley & Sons Ltd.)
Databáze: MEDLINE
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