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

By Evgenia V. Kriventseva, D. Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, R. Dias, Felipe A. Simão, E. Zdobnov. 2018

1,000 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology, Pharmacology

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Eugene V. Koonin

Citations in the corpus

Computed structures of core eukaryotic protein complexes (2021, methodology): “To distinguish orthologs from paralogs, we started from OrthoDB ( 18 ), a hierarchical catalog of orthologs across 1271 eukaryote genomes, and supplemented each orthologous group with sequences from 4325 eukaryote proteomes that we assembled from the National Center for Biotechnology Information (ht”
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020, positive): “We used OrthoDB v10 (23) as a source of protein sequences partitioned into relevant taxonomic divisions; particularly, we used plant division for A. thaliana , arthropod division for D. melanogaster , etc. (Table 2).”
TSEBRA: transcript selector for BRAKER (2021, background): “For example, the NCBI Sequence Read Archive (SRA) [6] hosts more than 36 petabytes of data, while the protein database OrthoDB [7] contains more than 37 million sequences.”
COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020, background): “Although there are several other databases of orthologous proteins in bacteria and archaea, such as eggNOG (49), KEGG Orthology (50,51), OMA (52,53), OrthoDB (54) and MBGD (55), which cover a wider selection of organisms than the COGs and provide comprehensive, automated functional annotation of the”
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, positive): “We used the OrthoDB database (34) as a source of protein data.”
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes (2021, background): “(Kriventseva et al. 2019; Zdobnov et al. 2021), providing coverage of many more lineages and a revised baseline with increased data sampling.”
Identification of mobile genetic elements with geNomad (2023, positive): “Our approach involved retrieving eukaryotic proteins belonging to ortholog groups from OrthoDB 71 (version 10.1) and removed the ones that corresponded to typical viral genes, resulting in a total of 16,928,157 eukaryotic proteins.”