First published: 17 January 2002. Cited by: 2911. Figures; Related.

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 in Brassica rapa and their evolution in plants. A total of 49 BrCPKs, 14 BrCRKs, 3 BrPPCKs, 5 BrPEPRKs, and 56 BrSnRKs were identified in B. 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 of BrCDPK-SnRK genes is dynamic in different tissues as well as in response to abiotic stresses, demonstrating their important roles in development in B. In summary, this study provides genome-wide insight into the evolutionary history and mechanisms of CDPK-SnRK genes following whole-genome triplication in B.

Identification and classification of the CDPK-SnRK superfamily of protein kinases in Brassica rapa and comparative analyses In this study, genome-wide analysis of CDPK-SnRK gene family has been performed on the basis of the completed B. Rapa genome sequence (Wang et al., ). Based on previously reported methods (Harmon et al.,; Hrabak et al., ), the homogeneous candidate CDPK-SnRK genes between Brassica rapa and other species were identified by BLASTP (Supplementary Table ). Subsequently, all candidate protein sequences were subjected to Pfam and SMART analyses. Finally, we identified 49 BrCPKs, 14 BrCRKs, 3 BrPPCKs, 5 BrPEPRKs, and 56 BrSnRKs named according to nomenclature proposed for CDPK-SnRK genes (Supplementary Table ).

To better understand the expansion and evolutionary history of CDPK-SnRK genes in B. Rapa, genes were also identified in 16 other species representing the major clades of plants. The evolutionary relationships of the species and the number of CDPK-SnRK genes are shown in Figure. The data show that Glycine max contained the highest number of CDPK-SnRK genes (200), followed by Z.

Mays (193) and M. Truncatula (188) (Figure ). Bmw ibus interface program software pdf. Trichopoda, a basal angiosperm species that was the single living representative of the sister lineage to all other extant flowering plants, contained the lowest number of CDPK-SnRK genes (28) in Angiospermae.

The reason is that it originated prior to the split of eudicots and monocots and has not experienced any whole genome duplication (WGD), while the other 12 angiosperms had several rounds of WGDs/triplications after their split from A. Furthermore, the number of CDPK-SnRK genes in algae, Bryophyta and Pteridophyta was less than that in Angiospermae. This phenomenon was also caused by several WGD events that occurred during angiosperm evolution (Figure ). These results indicated that the expansion of the CDPK-SnRK family from angiosperms mainly relied on large-scale DNA rearrangements, namely, WGDs. The elevated duplication frequency and increased retention of CDPK-SnRK genes also contributed to neofunctionalization and caused them to gain important functions in angiosperm development. Characteristics of structure, and expansion analysis of BrCDPK-SnRK proteins To investigate the extent of lineage-specific expansion of the CDPK-SnRK genes in B.

Buku pengantar teknik industri pdf file5338971. Rapa, phylogenetic trees were constructed using the maximum likelihood method (Figure ). The phylogenetic tree showed that all the CDPK-SnRK genes were clustered into five distinct gene classes (CPK, CRK, PEPRK, PPCK, SnRK) (Figure ), while the CPK family was divided into four groups (I, II, III, and IV) and the SnRK family was classified into three groups (SnRK1, SnRK2, and SnRK3), consistent with the reports in A. Thaliana (Hrabak et al., ).

Rapa, the CPK, CRK, PEPRK, PPCK, and SnRK gene families contained 49 members, 14 members, 3 members, 5 members, and 56 members, respectively, whereas in A. Thaliana, the CPK, CRK, PEPRK, PPCK, and SnRK families contained 34 members, 8 members, 2 members, 2 members, and 39 members, respectively. Next, the synteny of CDPK-SnRK genes between A. Thaliana and three subgenomes in B. Rapa was analyzed. There were 34 CPK, 8 CRK, 2 PEPRK, 2 PPCK, and 38 SnRK genes on the conserved collinear block (Supplementary Table ). Meanwhile, 2 CPKs, 2 CRKs, 1 PEPRK, 1 PPCK, and 3 SnRKs were retained completely; conversely, 4 CPKs and 3 SnRKs from B.