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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F23%3A00577005" target="_blank" >RIV/61388971:_____/23:00577005 - isvavai.cz</a>

Alternative codes found

RIV/68407700:21230/23:00367788 RIV/00216208:11310/23:10469817

Result on the web

<a href="https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13852" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13852</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/1755-0998.13852" target="_blank" >10.1111/1755-0998.13852</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10606 - Microbiology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2023

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Molecular Ecology Resources

ISSN

1755-098X

e-ISSN

1755-0998

Volume of the periodical

23

Issue of the periodical within the volume

8

Country of publishing house

GB - UNITED KINGDOM

Number of pages

12

Pages from-to

1800-1811

UT code for WoS article

001045828600001

EID of the result in the Scopus database

2-s2.0-85167618234