Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis.
Polygalacturonases (PGs) participate in pectin disassembly of cell wall and belong to one of the largest hydrolase families in plants. In this study, we identified 99 PG genes in Brassica rapa. Comprehensive analysis of phylogeny, gene structures, physico-chemical properties and coding sequence evolution demonstrated that plant PGs should be classified into seven divergent clades and each clade's members had specific sequence and structure characteristics, and/or were under specific selection pressures. Genomic distribution and retention rate analysis implied duplication events and biased retention contributed to PG family's expansion. Promoter divergence analysis using "shared motif method" revealed a significant correlation between regulatory and coding sequence evolution of PGs, and proved Clades A and E were of ancient origin. Quantitative real-time PCR analysis showed that expression patterns of PGs displayed group specificities in B. rapa. Particularly, nearly half of PG family members, especially those of Clades C, D and F, closely relates to reproductive development. Most duplicates showed similar expression profiles, suggesting dosage constraints accounted for preservation after duplication. Promoter-GUS assay further indicated PGs' extensive roles and possible redundancy during reproductive development. This work can provide a scientific classification of plant PGs, dissect the internal relationships between their evolution and expressions, and promote functional researches.
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. liangying8759@163.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. liangying8759@163.com.
Ying
Y
Liang
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. yuyoujian@gmail.com.|Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Lin'an, 311300, China. yuyoujian@gmail.com.
Youjian
Y
Yu
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. 375947388@qq.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. 375947388@qq.com.
Xiuping
X
Shen
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. dheng.0239@163.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. dheng.0239@163.com.
Heng
H
Dong
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. mllv2009@126.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. mllv2009@126.com.
Meiling
M
Lyu
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. xuyuanchicao@163.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. xuyuanchicao@163.com.
Liai
L
Xu
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. ramblermzm@126.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. ramblermzm@126.com.
Zhiming
Z
Ma
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. 2860637523@qq.com.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. 2860637523@qq.com.
Tingting
T
Liu
Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China. jshcao@zju.edu.cn.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310058, China. jshcao@zju.edu.cn.
Jiashu
J
Cao
D029741:Brassica rapa / Q000145:classification / Q000201:enzymology* / Q000235:genetics*; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D020440:Gene Duplication; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008957:Models, Genetic; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D030821:Plants, Genetically Modified; D011096:Polygalacturonase / Q000235:genetics*; D011401:Promoter Regions, Genetic; D013997:Time Factors
D010940:Plant Proteins; D011096:Polygalacturonase
Brassica rapa; Expression characteristics; Polygalacturonase gene family; Promoter divergence; Protein evolution