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Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histori...

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Detalles Bibliográficos
Autores principales: Ames, Ryan M., Money, Daniel, Lovell, Simon C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055711/
https://www.ncbi.nlm.nih.gov/pubmed/24921666
http://dx.doi.org/10.1371/journal.pone.0099480
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author Ames, Ryan M.
Money, Daniel
Lovell, Simon C.
author_facet Ames, Ryan M.
Money, Daniel
Lovell, Simon C.
author_sort Ames, Ryan M.
collection PubMed
description The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes.
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spelling pubmed-40557112014-06-18 Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions Ames, Ryan M. Money, Daniel Lovell, Simon C. PLoS One Research Article The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes. Public Library of Science 2014-06-12 /pmc/articles/PMC4055711/ /pubmed/24921666 http://dx.doi.org/10.1371/journal.pone.0099480 Text en © 2014 Ames et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ames, Ryan M.
Money, Daniel
Lovell, Simon C.
Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title_full Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title_fullStr Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title_full_unstemmed Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title_short Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
title_sort inferring gene family histories in yeast identifies lineage specific expansions
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4055711/
https://www.ncbi.nlm.nih.gov/pubmed/24921666
http://dx.doi.org/10.1371/journal.pone.0099480
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