A systematic search for positive selection in higher plants (Embryophytes)

BACKGROUND: Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples h...

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Những tác giả chính: Roth, Christian, Liberles, David A
Định dạng: Bài viết
Ngôn ngữ:English
Được phát hành: BioMed Central 2006
Những chủ đề:
Research Article
Truy cập trực tuyến:https://ncbi.nlm.nih.gov/pmc/articles/PMC1540423/
https://ncbi.nlm.nih.gov/pubmed/16784532
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/1471-2229-6-12
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spelling pubmed-15404232006-08-12 A systematic search for positive selection in higher plants (Embryophytes) Roth, Christian Liberles, David A BMC Plant Biol Research Article BACKGROUND: Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. RESULTS: Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >>1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (Magnoliophytes) without saturation of 4- fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta- sheets, but were less negative and more variant on the surface and away from the hydrophobic core. CONCLUSION: Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes. BioMed Central 2006-06-19 /pmc/articles/PMC1540423/ /pubmed/16784532 http://dx.doi.org/10.1186/1471-2229-6-12 Text en Copyright © 2006 Roth and Liberles; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
institution US National Library of Medicine
collection PubMed Central
language English
format Article
topic Research Article
spellingShingle Research Article
Roth, Christian
Liberles, David A
A systematic search for positive selection in higher plants (Embryophytes)
description BACKGROUND: Previously, a database characterizing examples of Embryophyte gene family lineages showing evidence of positive selection was reported. Of the gene family trees, 138 Embryophyte branches showed Ka/Ks>>1 and are candidates for functional adaptation. The database and these examples have now been studied in further detail to better understand the molecular basis for plant genome evolution. RESULTS: Neutral modeling showed an excess of positive and/or negative selection in the database over a neutral expectation centered on the mean Ka/Ks ratio. Out of 673 families with assigned structures, 490 have at least one branch with Ka/Ks >>1 in a region of the protein, enabling a picture of selective pressures delineated by protein structure. Most gene families allowed reconstruction back to the last common ancestor of flowering plants (Magnoliophytes) without saturation of 4- fold degenerate codon position. Positive selection occurred in a wide variety of gene families with different functions, including in the self incompatibility locus, in defense against pathogens, in embryogenesis, in cold acclimation, and in electrontransport. Structurally, selective pressures were similar between alpha-helices and beta- sheets, but were less negative and more variant on the surface and away from the hydrophobic core. CONCLUSION: Positive selection was detected statistically significantly in a small and nonrandom minority of gene families in a systematic analysis of embryophyte gene families. More sensitive methods increased the level of positive selection that was detected and presented a structural basis for the role of positive selection in plant genomes.
author Roth, Christian
Liberles, David A
author_facet Roth, Christian
Liberles, David A
author_sort Roth, Christian
title A systematic search for positive selection in higher plants (Embryophytes)
title_short A systematic search for positive selection in higher plants (Embryophytes)
title_full A systematic search for positive selection in higher plants (Embryophytes)
title_fullStr A systematic search for positive selection in higher plants (Embryophytes)
title_full_unstemmed A systematic search for positive selection in higher plants (Embryophytes)
title_sort systematic search for positive selection in higher plants (embryophytes)
publisher BioMed Central
publisher_facet BioMed Central
publishDate 2006
url https://ncbi.nlm.nih.gov/pmc/articles/PMC1540423/
https://ncbi.nlm.nih.gov/pubmed/16784532
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1186/1471-2229-6-12
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