Cargando…

Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana

Gene duplication is an important mechanism for the origination of functional novelties in organisms. We performed a comparative genome analysis to systematically estimate recent lineage specific gene duplication events in Arabidopsis thaliana and further investigate whether and how these new duplica...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Jun, Marowsky, Nicholas C., Fan, Chuanzhu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756979/
https://www.ncbi.nlm.nih.gov/pubmed/24009676
http://dx.doi.org/10.1371/journal.pone.0072362
_version_ 1782282148272668672
author Wang, Jun
Marowsky, Nicholas C.
Fan, Chuanzhu
author_facet Wang, Jun
Marowsky, Nicholas C.
Fan, Chuanzhu
author_sort Wang, Jun
collection PubMed
description Gene duplication is an important mechanism for the origination of functional novelties in organisms. We performed a comparative genome analysis to systematically estimate recent lineage specific gene duplication events in Arabidopsis thaliana and further investigate whether and how these new duplicate genes (NDGs) play a functional role in the evolution and adaption of A. thaliana. We accomplished this using syntenic relationship among four closely related species, A. thaliana, A. lyrata, Capsella rubella and Brassica rapa. We identified 100 NDGs, showing clear origination patterns, whose parental genes are located in syntenic regions and/or have clear orthologs in at least one of three outgroup species. All 100 NDGs were transcribed and under functional constraints, while 24% of the NDGs have differential expression patterns compared to their parental genes. We explored the underlying evolutionary forces of these paralogous pairs through conducting neutrality tests with sequence divergence and polymorphism data. Evolution of about 15% of NDGs appeared to be driven by natural selection. Moreover, we found that 3 NDGs not only altered their expression patterns when compared with parental genes, but also evolved under positive selection. We investigated the underlying mechanisms driving the differential expression of NDGs and their parents, and found a number of NDGs had different cis-elements and methylation patterns from their parental genes. Overall, we demonstrated that NDGs acquired divergent cis-elements and methylation patterns and may experience sub-functionalization or neo-functionalization influencing the evolution and adaption of A. thaliana.
format Online
Article
Text
id pubmed-3756979
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-37569792013-09-05 Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana Wang, Jun Marowsky, Nicholas C. Fan, Chuanzhu PLoS One Research Article Gene duplication is an important mechanism for the origination of functional novelties in organisms. We performed a comparative genome analysis to systematically estimate recent lineage specific gene duplication events in Arabidopsis thaliana and further investigate whether and how these new duplicate genes (NDGs) play a functional role in the evolution and adaption of A. thaliana. We accomplished this using syntenic relationship among four closely related species, A. thaliana, A. lyrata, Capsella rubella and Brassica rapa. We identified 100 NDGs, showing clear origination patterns, whose parental genes are located in syntenic regions and/or have clear orthologs in at least one of three outgroup species. All 100 NDGs were transcribed and under functional constraints, while 24% of the NDGs have differential expression patterns compared to their parental genes. We explored the underlying evolutionary forces of these paralogous pairs through conducting neutrality tests with sequence divergence and polymorphism data. Evolution of about 15% of NDGs appeared to be driven by natural selection. Moreover, we found that 3 NDGs not only altered their expression patterns when compared with parental genes, but also evolved under positive selection. We investigated the underlying mechanisms driving the differential expression of NDGs and their parents, and found a number of NDGs had different cis-elements and methylation patterns from their parental genes. Overall, we demonstrated that NDGs acquired divergent cis-elements and methylation patterns and may experience sub-functionalization or neo-functionalization influencing the evolution and adaption of A. thaliana. Public Library of Science 2013-08-29 /pmc/articles/PMC3756979/ /pubmed/24009676 http://dx.doi.org/10.1371/journal.pone.0072362 Text en © 2013 Wang 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
Wang, Jun
Marowsky, Nicholas C.
Fan, Chuanzhu
Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title_full Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title_fullStr Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title_full_unstemmed Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title_short Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in Arabidopsis thaliana
title_sort divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in arabidopsis thaliana
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756979/
https://www.ncbi.nlm.nih.gov/pubmed/24009676
http://dx.doi.org/10.1371/journal.pone.0072362
work_keys_str_mv AT wangjun divergentevolutionaryandexpressionpatternsbetweenlineagespecificnewduplicategenesandtheirparentalparalogsinarabidopsisthaliana
AT marowskynicholasc divergentevolutionaryandexpressionpatternsbetweenlineagespecificnewduplicategenesandtheirparentalparalogsinarabidopsisthaliana
AT fanchuanzhu divergentevolutionaryandexpressionpatternsbetweenlineagespecificnewduplicategenesandtheirparentalparalogsinarabidopsisthaliana