Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.

It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous gen...

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Autores principales:	Yue Guo, Jing Liu, Xingna Wang, Ying Li, Xilin Hou, Jianchang Du
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a03ef6e621d94fecb88fedec61751426
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spelling	oai:doaj.org-article:a03ef6e621d94fecb88fedec617514262021-12-02T20:13:45ZDistribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.1932-620310.1371/journal.pone.0256120https://doaj.org/article/a03ef6e621d94fecb88fedec617514262021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0256120https://doaj.org/toc/1932-6203It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous genes between Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea), and identified 468 putative PSGs. Our data show that, (1) PSGs are enriched in plant hormone signal transduction pathway and the transcription factor family; (2) PSGs are significantly lower expressed than randomly selected non-PSGs; (3) PSGs with tissue specificity are significantly higher expressed in the callus and reproductive tissues (flower and silique) than in vegetable tissues (root, stem and leaf); (4) the proportion of PSGs is positively correlated with the number of retained triplication gene copies, but the expression level of PSGs decay with the increasing of triplication gene copies; (5) the CG and CHG methylation levels of PSGs are significantly higher in introns and UTRs than in the promoter and exon regions; (6) the percent of transposable element is in proportion to the methylation level, and DNA methylation (especially in the CG content) has the tendency to reduce the expression of PSGs. This study provides insights into the characteristics, evolution, function, expression and methylation of PSGs in B. rapa.Yue GuoJing LiuXingna WangYing LiXilin HouJianchang DuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0256120 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yue Guo Jing Liu Xingna Wang Ying Li Xilin Hou Jianchang Du Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
description	It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous genes between Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea), and identified 468 putative PSGs. Our data show that, (1) PSGs are enriched in plant hormone signal transduction pathway and the transcription factor family; (2) PSGs are significantly lower expressed than randomly selected non-PSGs; (3) PSGs with tissue specificity are significantly higher expressed in the callus and reproductive tissues (flower and silique) than in vegetable tissues (root, stem and leaf); (4) the proportion of PSGs is positively correlated with the number of retained triplication gene copies, but the expression level of PSGs decay with the increasing of triplication gene copies; (5) the CG and CHG methylation levels of PSGs are significantly higher in introns and UTRs than in the promoter and exon regions; (6) the percent of transposable element is in proportion to the methylation level, and DNA methylation (especially in the CG content) has the tendency to reduce the expression of PSGs. This study provides insights into the characteristics, evolution, function, expression and methylation of PSGs in B. rapa.
format	article
author	Yue Guo Jing Liu Xingna Wang Ying Li Xilin Hou Jianchang Du
author_facet	Yue Guo Jing Liu Xingna Wang Ying Li Xilin Hou Jianchang Du
author_sort	Yue Guo
title	Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
title_short	Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
title_full	Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
title_fullStr	Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
title_full_unstemmed	Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.
title_sort	distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in brassica rapa.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/a03ef6e621d94fecb88fedec61751426
work_keys_str_mv	AT yueguo distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa AT jingliu distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa AT xingnawang distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa AT yingli distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa AT xilinhou distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa AT jianchangdu distributionexpressionandmethylationanalysisofpositivelyselectedgenesprovidesinsightsintotheevolutioninbrassicarapa
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Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa.

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