Advances and applications in the quest for orthologs

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  • dc.contributor.author Glover, Natasha
  • dc.contributor.author Dessimoz, Christophe
  • dc.contributor.author Ebersberger, Ingo
  • dc.contributor.author Forslund, Sofia K.
  • dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
  • dc.contributor.author Huerta Cepas, Jaime
  • dc.contributor.author Martin, Maria-Jesus
  • dc.contributor.author Muffato, Matthieu
  • dc.contributor.author Patricio, Mateus
  • dc.contributor.author Pereira, Cecile
  • dc.contributor.author Sousa da Silva, Alan
  • dc.contributor.author Wang, Yan-Dong
  • dc.contributor.author Sonnhammer, Erik
  • dc.contributor.author Thomas, Paul D.
  • dc.date.accessioned 2020-03-31T07:46:23Z
  • dc.date.available 2020-03-31T07:46:23Z
  • dc.date.issued 2019
  • dc.description.abstract Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
  • dc.description.sponsorship We thank the Society for Molecular Biology and Evolution for supporting the SMBE-EGF Symposium, and the University of Southern California for supporting the QFO5 meeting. We wish to acknowledge the following support for attending the meetings and/or writing this manuscript: National Institutes of Health (grant HG002273 for P.D.T.; HG007822 for M.J.M. and A.S.d.S.; GM122480, HD085901, DK110520 for E.M.M.; GM123683 for C.M.), Wellcome Trust (grant WT108749/Z/15/Z for M.M. and M.P.), Swiss National Science Foundation (grant 150654 for C.D.), European Commission (contract 676559 for S.C.G.), Welch Foundation (grant F-1515 for E.M.M.), European Molecular Biology Laboratory (for M.J.M., M.M., M.P.), and National Bioscience Database Center and Japan Science and Technology Agency (for I.U.).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Advances and applications in the quest for orthologs. Mol Biol Evol. 2019; 36(10):2157-64. DOI: 10.1093/molbev/msz150
  • dc.identifier.doi http://dx.doi.org/10.1093/molbev/msz150
  • dc.identifier.issn 0737-4038
  • dc.identifier.uri http://hdl.handle.net/10230/44121
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Mol Biol Evol. 2019; 36(10):2157-64
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
  • dc.rights © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Gene family
  • dc.subject.keyword Genome evolution
  • dc.subject.keyword Orthology
  • dc.title Advances and applications in the quest for orthologs
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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