Abstract
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.
Highlights
The adaptive evolution of genes and genomes determine the morphology, behavior, physiological adaptation, species divergence and evolutionary innovation [1]
The densities of positively selected genes (PSGs) were found to be associated with chromosomal locations according to both Chi-square test (P = 0.0179) and Fisher exact probability test (P = 0.0150) (S1 Table), indicating that genomic location is a factor influencing the distribution of PSGs
The data show that, relative to PSGs with constitutive expression, PSGs with tissue specificity are significantly non-randomly distributed, indicating that tissue specific PSGs are highly unevenly located along B. rapa chromosomes (Chi-square test and Fisher exact probability test, P < 0.05; S2–S4 Figs)
Summary
The adaptive evolution of genes and genomes determine the morphology, behavior, physiological adaptation, species divergence and evolutionary innovation [1]. The detection of genes under positive selection is important to understand the molecular basis underlying organism adaptive evolution [2]. Such positively selected genes (PSGs) usually carry advantageous mutations, which are favorable for individuals to adapt environment, to survive. Science and Technology Innovation Fund (CX203009 awarded to Na Yuan & Jianchang Du). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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