DrosOMA: the Drosophila Orthologous Matrix browser

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.

Figure 1.. Species phylogeny and orthology classifications across 36 Drosophila and four outgroup species.

The time-calibrated species phylogeny (left) shows the estimated evolutionary relationships amongst the set of 40 species spanning approximately 60 million years since the last common ancestor of the Drosophila genus. The dashed line indicates the Drosophila and Culicidae last common ancestor but for visualisation is not placed according to the timescale. The barchart (right) shows counts of genes per species categorised according to their orthology type based on root-level hierarchical orthologous groups (HOGs). Analysis of the root-level HOGs shows counts of proteins per species belonging to universal single-copy HOGs (Single-copy All), universal but variable-copy-number HOGs (Orthologues All), non-universal HOGs with outgroup species orthologues ( Drosophila & Culicidae), mosquito-only orthologues ( Culicidae Only), as well as drosophilid-specific HOGs with orthologues from all ( Drosophila All), the majority ( Drosophila Majority), or the minority ( Drosophila Minority) of the 36 Drosophila species. This leaves an average of 527 ±392 proteins per drosophilid species with no identifiable orthologues, i.e. annotated protein-coding genes that, given the set of species under consideration, appear to be species-specific with no traceable common ancestry. Branch lengths are shown in millions of years; all nodes received 100% bootstrap support except * with 95%; D. Drosophila; An. Anopheles; Ae. Aedes; Minority <18 drosophilids; Majority ≥18 drosophilids.

Figure 2.. Example orthologous group and gene information views available from the DrosOMA browser.

(A) The simple search entry point for DrosOMA allows for text searches with gene names, descriptors, or identifiers, as well as with protein sequences. (B) Visualising information for Hierarchical Orthologous Groups (HOGs) can be guided by the species phylogeny (left) showing counts of orthologues per species, or as a table (right) with protein identifiers and cartoons showing domain architectures. (C) The gene view page displays available information for genes of interest and their mappings to external databases.

Figure 3.. Example additional analysis views available from the DrosOMA browser.

(A) Multiple sequence alignments of proteins from hierarchical orthologous groups (HOGs) or OMA Groups can be generated, visualised, explored, and downloaded using the DrosOMA Browser. (B) Local gene synteny conservation can be visualised to explore how orthologues have maintained or shuffled their local arrangements in the genomes of each considered species.