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Inferring Orthologs: Open Questions and Perspectives
With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Libertas Academica
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778853/ https://www.ncbi.nlm.nih.gov/pubmed/26966373 http://dx.doi.org/10.4137/GEI.S37925 |
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author | Tekaia, Fredj |
author_facet | Tekaia, Fredj |
author_sort | Tekaia, Fredj |
collection | PubMed |
description | With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny. |
format | Online Article Text |
id | pubmed-4778853 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
spelling | pubmed-47788532016-03-10 Inferring Orthologs: Open Questions and Perspectives Tekaia, Fredj Genomics Insights Review With the increasing number of sequenced genomes and their comparisons, the detection of orthologs is crucial for reliable functional annotation and evolutionary analyses of genes and species. Yet, the dynamic remodeling of genome content through gain, loss, transfer of genes, and segmental and whole-genome duplication hinders reliable orthology detection. Moreover, the lack of direct functional evidence and the questionable quality of some available genome sequences and annotations present additional difficulties to assess orthology. This article reviews the existing computational methods and their potential accuracy in the high-throughput era of genome sequencing and anticipates open questions in terms of methodology, reliability, and computation. Appropriate taxon sampling together with combination of methods based on similarity, phylogeny, synteny, and evolutionary knowledge that may help detecting speciation events appears to be the most accurate strategy. This review also raises perspectives on the potential determination of orthology throughout the whole species phylogeny. Libertas Academica 2016-02-25 /pmc/articles/PMC4778853/ /pubmed/26966373 http://dx.doi.org/10.4137/GEI.S37925 Text en © 2016 the author(s), publisher and licensee Libertas Academica Ltd. This is an open-access article distributed under the terms of the Creative Commons CC-BY-NC 3.0 License. |
spellingShingle | Review Tekaia, Fredj Inferring Orthologs: Open Questions and Perspectives |
title | Inferring Orthologs: Open Questions and Perspectives |
title_full | Inferring Orthologs: Open Questions and Perspectives |
title_fullStr | Inferring Orthologs: Open Questions and Perspectives |
title_full_unstemmed | Inferring Orthologs: Open Questions and Perspectives |
title_short | Inferring Orthologs: Open Questions and Perspectives |
title_sort | inferring orthologs: open questions and perspectives |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778853/ https://www.ncbi.nlm.nih.gov/pubmed/26966373 http://dx.doi.org/10.4137/GEI.S37925 |
work_keys_str_mv | AT tekaiafredj inferringorthologsopenquestionsandperspectives |