Advances and Applications in the Quest for Orthologs

By Natasha M. Glover, Christophe Dessimoz, Ingo Ebersberger, Sofia K. Forslund, Toni Gabaldón, Jaime Huerta-Cepas, Maria Jesus Martin, Matthieu Muffato, Mateus Patricio, Cécile Pereira and 4 more. 2019

84 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

Sensitive protein alignments at tree-of-life scale using DIAMOND (2021, methodology): “0.7) uses two seed shapes of weight 10 for its fast mode, 16 shapes of weight 8 and 14 shapes of weight 7 for its sensitive and very-sensitive modes, respectively, and 64 shapes of weight 7 for its ultra-sensitive mode.”
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL (2019, background): “Introduction Gene classification based on evolutionary history is essential for many aspects of comparative and functional genomics - reviewed in (Gabaldón & Koonin, 2013); (Glover et al., 2019).”
Alliance of Genome Resources Portal: unified model organism research platform (2019, methodology): “Ortholog inferences from methods benchmarked by the Quest for Orthologs Consortium (11), as well as manually curated ortholog inferences from HGNC and ZFIN, have been incorporated into a tabulated presentation (Figure 4).”
Identifying orthologs with OMA: A primer (2020, background): “Among many applications (reviewed by Glover et al.(2)), orthologs are useful to infer species trees (reviewed by Fernandez et al.”