Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.

Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphr...

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Autores principales:	Jian Zhang, Penghui Xie, Martin Lascoux, Thomas R Meagher, Jianquan Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dc8d9bc0c95546c1ac4b30026c66ff89
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spelling	oai:doaj.org-article:dc8d9bc0c95546c1ac4b30026c66ff892021-11-18T07:42:12ZRapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.1932-620310.1371/journal.pone.0066370https://doaj.org/article/dc8d9bc0c95546c1ac4b30026c66ff892013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23776666/?tool=EBIhttps://doaj.org/toc/1932-6203Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in 'responses to stress', 'ubiquitin-dependent protein catabolic processes', and 'biological regulation'. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.Jian ZhangPenghui XieMartin LascouxThomas R MeagherJianquan LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 6, p e66370 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jian Zhang Penghui Xie Martin Lascoux Thomas R Meagher Jianquan Liu Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
description	Understanding which genes have evolved rapidly with the recent tree speciation in arid habitats can provide valuable insights into different adaptation mechanisms. We employed a comparative evolutionary analysis of expressed sequence tags (ESTs) from two desert poplars, Populus pruinosa and P. euphratica, which diverged in the recent past. Following an approach taken previously with P. euphratica, we conducted a deep transcriptomic analysis of P. pruinosa. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of two types of callus and desert-grown trees. De novo assembly generated 114,866 high-quality unique sequences using Solexa sequence data. Following assembly we were able to identify, with high confidence, 2859 orthologous sequence pairs between the two species. Based on the ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, we identified a total of 84 (2.9%) ortholog pairs exhibiting rapid evolution with signs of strong selection (Ka/Ks>1). Genes homologous to these ortholog pairs in model species are mainly involved in 'responses to stress', 'ubiquitin-dependent protein catabolic processes', and 'biological regulation'. Finally, we examined the expression patterns of candidate genes with rapid evolution in response to salt stress. Only one pair of orthologs up-regulated their expression in both species while three and four genes were found to up-regulated in P. pruinosa and in P. euphratica respectively. Our findings together suggest that the genes at the same category or network but with differentiated expressions or functions may have evolved rapidly during adaptive divergence of the two species to differentiated salty desert habitats.
format	article
author	Jian Zhang Penghui Xie Martin Lascoux Thomas R Meagher Jianquan Liu
author_facet	Jian Zhang Penghui Xie Martin Lascoux Thomas R Meagher Jianquan Liu
author_sort	Jian Zhang
title	Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
title_short	Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
title_full	Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
title_fullStr	Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
title_full_unstemmed	Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.
title_sort	rapidly evolving genes and stress adaptation of two desert poplars, populus euphratica and p. pruinosa.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/dc8d9bc0c95546c1ac4b30026c66ff89
work_keys_str_mv	AT jianzhang rapidlyevolvinggenesandstressadaptationoftwodesertpoplarspopuluseuphraticaandppruinosa AT penghuixie rapidlyevolvinggenesandstressadaptationoftwodesertpoplarspopuluseuphraticaandppruinosa AT martinlascoux rapidlyevolvinggenesandstressadaptationoftwodesertpoplarspopuluseuphraticaandppruinosa AT thomasrmeagher rapidlyevolvinggenesandstressadaptationoftwodesertpoplarspopuluseuphraticaandppruinosa AT jianquanliu rapidlyevolvinggenesandstressadaptationoftwodesertpoplarspopuluseuphraticaandppruinosa
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Rapidly evolving genes and stress adaptation of two desert poplars, Populus euphratica and P. pruinosa.

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