Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages

Objectives Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. Data description We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.

Automated summary

Identifying orthology relationships among sequences is crucial for understanding evolution, diversity of life, and ancestral relationships among organisms. This study assembled a dataset tailored for phylogenomic research on algae and photosynthetic eukaryotes, integrating organellar data and distinguishing between gene paralogs. Through OrthoFinder analysis, top-quality and taxonomically diverse proteomes were used to identify orthogroups, functionally annotated with eggNOG, and aligned for phylogenetic tree computation, with a focus on plastid-bearing organisms.