Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica.
It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (Ka) and the rates of synonymous substitution (Ks) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (Ka/Ks), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica.
Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
Yue
Y
Guo
Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
Jing
J
Liu
Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture of People's Republic of China, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
Jiefu
J
Zhang
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
Shengyi
S
Liu
Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.|Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture of People's Republic of China, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.|Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
Jianchang
J
Du
D001937:Brassica / Q000235:genetics* / Q000378:metabolism*; D019143:Evolution, Molecular; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*
D010940:Plant Proteins

Brassica
; nonsynonymous substitution; positive selection; purifying selection; synonymous substitution