DrosOMA: the Drosophila Orthologous Matrix browser

Antonin Thiébaut; Adrian M Altenhoff; Giulia Campli; Natasha Glover; Christophe Dessimoz; Robert M Waterhouse

doi:10.12688/f1000research.135250.2

DrosOMA: the Drosophila Orthologous Matrix browser

F1000Res. 2024 Jan 16:12:936. doi: 10.12688/f1000research.135250.2. eCollection 2023.

Authors

Antonin Thiébaut¹, Adrian M Altenhoff², Giulia Campli¹, Natasha Glover³, Christophe Dessimoz³, Robert M Waterhouse¹

Affiliations

¹ Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
² Department of Computer Science, SIB Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland.
³ Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.

Abstract

Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.

Methods: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.

Results: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.

Conclusions: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.

Keywords: Drosophila; comparative genomics; database; gene families; orthologous groups; orthologues; orthology; synteny.

MeSH terms

Animals
Comparative Genomic Hybridization
Databases, Factual
Drosophila* / genetics
Evolution, Molecular*
Genomics

Associated data

figshare/10.6084/m9.figshare.23622507.v1

Grants and funding

This work was supported by the Swiss National Science Foundation Sinergia grants 186397 to CD and RMW, and 198691 to RMW, and by Swiss National Science Foundation grants 205085 to CD and PP00P3_202669 to RMW.