Mol Biol Evol.: auth.: group Dessimoz

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Mol Biol Evol. 2021 Apr 2;msab098. doi: 10.1093/molbev/msab098. Online ahead of print.

Ten years of collaborative progress in the Quest for Orthologs

Benjamin Linard 1 2, Ingo Ebersberger 3 4 5, Shawn E McGlynn 6 7, Natasha Glover 8 9 10, Tomohiro Mochizuki 6, Mateus Patricio 11, Odile Lecompte 12, Yannis Nevers 8 9 10, QFO Consortium; Paul D Thomas 13, Toni Gabaldón 14 15 16, Erik Sonnhammer 17, Christophe Dessimoz 8 9 10 18 19, Ikuo Uchiyama 20Affiliations expand

Abstract

Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology – evolutionary relatedness – is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) consortium. The 6th QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardisation and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit-from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.