Published online 23 October 2010 Nucleic Acids Research, 2011, Vol. 39, Database issue D283–D288 doi:10.1093/nar/gkq930 OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 Robert M. Waterhouse1,2, Evgeny M. Zdobnov1,2,3, Fredrik Tegenfeldt1,2, Jia Li1,2 and Evgenia V. Kriventseva1,2,* 1Department of Genetic Medicine and Development, University of Geneva Medical School, 2Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland and 3Imperial College London, South Kensington Campus, London, SW7 2AZ, UK Received September 15, 2010; Accepted September 27, 2010 ABSTRACT The concept of homology drives speculation on a gene’s function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation hom- ologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scale delineation of gene genealogies is a challenging task, and the numerous approaches to the problem reflect the importance of the concept of orthology as a cornerstone for comparative studies. Here, we present the updated OrthoDB catalog of eukaryotic orthologs delineated at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi (including the metazoa level). New database features include functional annotations, and quan- tification of evolutionary divergence and relations among orthologous groups. The interface features extended phyletic profile querying and enhanced text-based searches. The ever-increasing sampling of sequenced eukaryotic genomes brings a clearer account of the majority of gene genealogies that will facilitate informed hypotheses of gene function in newly sequenced genomes. Furthermore, uniform analysis across lineages as different as vertebrates, arthropods and fungi with divergence levels varying from several to hundreds of millions of years will provide essential data for uncovering and quantifying long-term trends of gene evolution. OrthoDB is freely accessible from http://cegg.unige.ch/orthodb. INTRODUCTION Recognizing similarities as evidence of shared ancestry describes the general biological concept of homology that can be applied speciﬁcally to genes encoded in complete genomes to delineate orthologs, the ‘equivalent’ genes in different species, and paralogs, gene duplicates within one genome (1–3). The rapidly increasing number of sequenced genomes presents a remarkable opportunity as well as a formidable challenge to resolve complex gene histories in unprecedented detail. As orthologous relations are deﬁned by speciation events where orthologs arise by vertical decent from a single gene of the last common ancestor, such classiﬁcations are inherently hierarchical. Gene duplication events after speciation disrupt the 1:1 correspondence of genes among species and lead to the formation of orthologous groups, comprised of all genes descended from a single gene of the last common ancestor. Many algorithms have been developed to apply these prin- ciples and meet the challenge of large-scale data analysis (4,5). These can be broadly classiﬁed into those that cluster the results from all-against-all pairwise sequence comparisons and those that employ phylogenetic tree-based methods. The growing number of different re- sources for cluster-based approaches [e.g. (6–12)], as well as for phylogenetic approaches [e.g. (13–20)], reﬂects the importance of ortholog identiﬁcation as a cornerstone of comparative genomics that drives evolutionary and molecular biology research. The preservation of orthologs across many species over long evolutionary periods, especially as single-copy genes, strongly supports hypotheses of conserved functionality (21). By contrast, duplication events may allow for func- tional divergence (22). Thus, although orthologous rela- tions are not deﬁned by gene function, inferences of common functions remain the most plausible evolutionary scenario and therefore justify one of the major objectives of orthology delineation: the tentative transfer of func- tional annotations from well-studied organisms to the newly sequenced species (23). Here, we present the update of OrthoDB (10), the hier- archical catalog of eukaryotic orthologs, featuring an expanded species sampling, extensive functional and *To whom correspondence should be addressed. Tel: +41 22 379 58 86; Fax: +41 22 379 57 06; Email: evgenia.kriventseva@isb-sib.ch The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.