LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins

Abstract The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not as...

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Bibliographic Details
Published inGenome biology and evolution Vol. 16; no. 11
Main Author Sobala, Łukasz F
Format Journal Article
LanguageEnglish
Published UK Oxford University Press 01.11.2024
Subjects
Animals
Biological Evolution
Databases, Protein
Eukaryota - genetics
Evolution, Molecular
Genome Resource
Metadata
Metagenomics
Proteins - genetics
Transcriptomics
eukaryote
evolution
metazoa
proteome
Online AccessGet full text
ISSN1759-6653
1759-6653
DOI10.1093/gbe/evae231

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Summary:Abstract The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well. Graphical abstract Graphical Abstract
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ISSN:1759-6653
1759-6653
DOI:10.1093/gbe/evae231