OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

Abstract

OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

“…The precise definition of a group of orthologous genes, however, depends on the particular method used, and several methods and algorithms to cluster orthologous genes have been proposed, including blast searches, Markov clustering, spectral clustering and hierarchical orthology. Several similarity-based methods are commonly used in phylogenetics and functional genomics, including orthomcl (Li, 2003), cog (Tatusov et al, 2003), inparanoid (O'Brien, 2005), oma (Roth, 2008), proteinortho (Lechner et al, 2011), eggnog (Powell et al, 2012), orthofinder (Emms & Kelly, 2015), orthograph (Petersen et al, 2017) and orthodb (Kriventseva et al, 2019). By contrast, phylogeny-based methods aim to identify orthologues by inferring the lowest common ancestor relationships between genes, which is performed by estimating a gene tree and identifying its speciation and duplication events using reconciliation with a species tree (Ullah et al, 2015).…”

The natural history of Get3‐like chaperones

“…Identifiers of Get3 and ArsA homologs were retrieved from KEGG Database (https://www.genome.jp/kegg/) and OrthoDB (https://www.orthodb.org). Identifiers of Get3 homologs with an α‐crystallin domain in land plants were retrieved using a blast search in land plants using the sequence of Nostoc Get3.…”

Sex chromosome evolution in muscid flies

“…For stable fly, we selected OrthoGroups from the OrthoDB annotation that contain a single D. melanogaster gene and a single S. calcitrans gene (Kriventseva et al, 2018;Olafson et al, 2019). For horn fly, we obtained annotated genes from the initial analysis of the genome, and we extracted the inferred D. melanogaster homologs for each gene (Konganti et al, 2018).…”