Advances and applications in the quest for orthologs

  • 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.

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Author:Natasha GloverORCiD, Christophe DessimozORCiDGND, Ingo EbersbergerORCiDGND, Sofia K. Forslund, Toni GabaldónORCiDGND, Jaime Huerta-Cepas, Maria-Jesus Martin, Matthieu Muffato, Mateus PatricioORCiD, Cécile Pereira, Alan Wilter Sousa da Silva, Yan Wang, Erik SonnhammerORCiD, Paul D. ThomasORCiD
URN:urn:nbn:de:hebis:30:3-533200
DOI:https://doi.org/10.1093/molbev/msz150
ISSN:1537-1719
ISSN:0737-4038
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/31241141
Parent Title (English):Molecular biology and evolution
Publisher:Oxford Univ. Press
Place of publication:Oxford
Contributor(s):Rebekah Rogers
Document Type:Article
Language:English
Year of Completion:2019
Date of first Publication:2019/06/27
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Contributing Corporation:Quest for Orthologs Consortium
Release Date:2020/03/25
Tag:gene family; genome evolution; orthology
Volume:36
Issue:10
Page Number:8
First Page:2157
Last Page:2164
Note:
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.
HeBIS-PPN:464892023
Institutes:Biowissenschaften / Biowissenschaften
Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Fachübergreifende Einrichtungen / Biodiversität und Klima Forschungszentrum (BiK-F)
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - Namensnennung 4.0