title: Comprehensive Analysis of the CDPK-SnRK Superfamily Genes in Chinese Cabbage and Its Evolutionary Implications in Plants.
abstract: The CDPK-SnRK (calcium-dependent protein kinase/Snf1-related protein kinase) gene superfamily plays important roles in signaling pathways for disease resistance and various stress responses, as indicated by emerging evidence. In this study, we constructed comparative analyses of gene structure, retention, expansion, whole-genome duplication (WGD) and expression patterns of CDPK-SnRK genes inBrassica rapaand their evolution in plants. A total of 49BrCPKs, 14BrCRKs, 3BrPPCKs, 5BrPEPRKs, and 56BrSnRKs were identified inB. rapa. All BrCDPK-SnRK proteins had highly conserved kinase domains. By statistical analysis of the number of CDPK-SnRK genes in each species, we found that the expansion of the CDPK-SnRK gene family started from angiosperms. Segmental duplication played a predominant role in CDPK-SnRK gene expansion. The analysis showed that PEPRK was more preferentially retained than other subfamilies and that CPK was retained similarly to SnRK. Among the CPKs and SnRKs, CPKIII and SnRK1 genes were more preferentially retained than other groups. CRK was closest to CPK, which may share a common evolutionary origin. In addition, we identified 196 CPK genes and 252 SnRK genes in 6 species, and their different expansion and evolution types were discovered. Furthermore, the expression ofBrCDPK-SnRKgenes is dynamic in different tissues as well as in response to abiotic stresses, demonstrating their important roles in development inB. rapa. In summary, this study provides genome-wide insight into the evolutionary history and mechanisms of CDPK-SnRK genes following whole-genome triplication inB. rapa.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University Nanjing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University Nanjing, China.
authors.forename: Wenli
authors.initials: W
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural UniversityNanjing, China; School of Life Science and Food Engineering, Huaiyin Institute of TechnologyHuaian, China.
authors.forename: Weike
authors.initials: W
authors.lastname: Duan
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University Nanjing, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University Nanjing, China.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
keywords: Brassica rapa; CDPK-SnRK genes; evolutionary conservation; evolutionary pattern; expression pattern; synteny analysis