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Genome-wide identification and expression analysis of calcium-dependent protein kinase and its closely related kinase genes in Capsicum annuum.

Cai H, Cheng J, Yan Y, Xiao Z, Li J, Mou S, Qiu A, Lai Y, Guan D, He S - Front Plant Sci (2015)

Bottom Line: Conserved sequence and exon-intron structures were found to be shared by pepper CDPKs within the same subfamily, and the expansion of the CDPK family in pepper was found to be due to segmental duplication events.Five CDPKs in the C. annuum variety CM334 were found to be mutated in the Chiltepin variety, and one CDPK present in CM334 was lost in Chiltepin.Our results lay the foundation for future functional characterization of pepper CDPK and its closely related gene families.

View Article: PubMed Central - PubMed

Affiliation: National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University Fuzhou, China ; College of Life Science, Fujian Agriculture and Forestry University Fuzhou, China.

ABSTRACT
As Ca2+ sensors and effectors, calcium-dependent protein kinases (CDPKs) play important roles in plant growth, development, and response to environmental cues. However, no CDPKs have been characterized in Capsicum annuum thus far. Herein, a genome wide comprehensive analysis of genes encoding CDPKs and CDPK-related protein kinases (CRKs) was performed in pepper, a total of 31 CDPK genes and five closely related kinase genes were identified, which were phylogenetically divided into four distinct subfamilies and unevenly distributed across nine chromosomes. Conserved sequence and exon-intron structures were found to be shared by pepper CDPKs within the same subfamily, and the expansion of the CDPK family in pepper was found to be due to segmental duplication events. Five CDPKs in the C. annuum variety CM334 were found to be mutated in the Chiltepin variety, and one CDPK present in CM334 was lost in Chiltepin. The majority of CDPK and CRK genes were expressed in different pepper tissues and developmental stages, and 10, 12, and 8 CDPK genes were transcriptionally modified by salt, heat, and Ralstonia solanacearum stresses, respectively. Furthermore, these genes were found to respond specifically to one stress as well as respond synergistically to two stresses or three stresses, suggesting that these CDPK genes might be involved in the specific or synergistic response of pepper to salt, heat, and R. solanacearum. Our results lay the foundation for future functional characterization of pepper CDPK and its closely related gene families.

No MeSH data available.


Related in: MedlinePlus

Intron-exon organization of the 31 CDPK and five CRK genes. The gene structures were analyzed using an online tool (http://gsds.cbi.pku.edu.cn/).
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Figure 3: Intron-exon organization of the 31 CDPK and five CRK genes. The gene structures were analyzed using an online tool (http://gsds.cbi.pku.edu.cn/).

Mentions: To obtain further insights into the possible structural evolution of CDPK genes in the pepper genome, diverse exon-intron organizations of CaCDPKs were compared. As shown in Figure 3 and Table 3, CaCDPKs clustered in the same subfamily shared very similar exon-intron structures. Most members of subfamily I possessed seven exons, with the exception of CaCDPK2 and CaCDPK17 (12 exons). Members in subfamily II harbored diverse numbers of exons: eight exons were found in CaCDPK3, CaCDPK5, CaCDPK10, and CaCDPK11, seven exons were found in CaCDPK7, CaCDPK23, CaCDPK26, and CaCDPK27, and five exons were found in CaCDPK14. In subfamily III, CaCDPK16, and CaCDPK18 had nine exons, CaCDPK1, CaCDPK24, and CaCDPK25 had eight exons, and CaCDPK9 had seven exons. The two members in subfamily IV both had 12 exons. The results indicate that CDPK genes with higher homogenous sequences tend to have the same numbers of exons, interestingly, members of subfamily I and subfamily IV have the same numbers of exons in pepper and cotton.


Genome-wide identification and expression analysis of calcium-dependent protein kinase and its closely related kinase genes in Capsicum annuum.

Cai H, Cheng J, Yan Y, Xiao Z, Li J, Mou S, Qiu A, Lai Y, Guan D, He S - Front Plant Sci (2015)

Intron-exon organization of the 31 CDPK and five CRK genes. The gene structures were analyzed using an online tool (http://gsds.cbi.pku.edu.cn/).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584942&req=5

Figure 3: Intron-exon organization of the 31 CDPK and five CRK genes. The gene structures were analyzed using an online tool (http://gsds.cbi.pku.edu.cn/).
Mentions: To obtain further insights into the possible structural evolution of CDPK genes in the pepper genome, diverse exon-intron organizations of CaCDPKs were compared. As shown in Figure 3 and Table 3, CaCDPKs clustered in the same subfamily shared very similar exon-intron structures. Most members of subfamily I possessed seven exons, with the exception of CaCDPK2 and CaCDPK17 (12 exons). Members in subfamily II harbored diverse numbers of exons: eight exons were found in CaCDPK3, CaCDPK5, CaCDPK10, and CaCDPK11, seven exons were found in CaCDPK7, CaCDPK23, CaCDPK26, and CaCDPK27, and five exons were found in CaCDPK14. In subfamily III, CaCDPK16, and CaCDPK18 had nine exons, CaCDPK1, CaCDPK24, and CaCDPK25 had eight exons, and CaCDPK9 had seven exons. The two members in subfamily IV both had 12 exons. The results indicate that CDPK genes with higher homogenous sequences tend to have the same numbers of exons, interestingly, members of subfamily I and subfamily IV have the same numbers of exons in pepper and cotton.

Bottom Line: Conserved sequence and exon-intron structures were found to be shared by pepper CDPKs within the same subfamily, and the expansion of the CDPK family in pepper was found to be due to segmental duplication events.Five CDPKs in the C. annuum variety CM334 were found to be mutated in the Chiltepin variety, and one CDPK present in CM334 was lost in Chiltepin.Our results lay the foundation for future functional characterization of pepper CDPK and its closely related gene families.

View Article: PubMed Central - PubMed

Affiliation: National Education Ministry, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University Fuzhou, China ; College of Life Science, Fujian Agriculture and Forestry University Fuzhou, China.

ABSTRACT
As Ca2+ sensors and effectors, calcium-dependent protein kinases (CDPKs) play important roles in plant growth, development, and response to environmental cues. However, no CDPKs have been characterized in Capsicum annuum thus far. Herein, a genome wide comprehensive analysis of genes encoding CDPKs and CDPK-related protein kinases (CRKs) was performed in pepper, a total of 31 CDPK genes and five closely related kinase genes were identified, which were phylogenetically divided into four distinct subfamilies and unevenly distributed across nine chromosomes. Conserved sequence and exon-intron structures were found to be shared by pepper CDPKs within the same subfamily, and the expansion of the CDPK family in pepper was found to be due to segmental duplication events. Five CDPKs in the C. annuum variety CM334 were found to be mutated in the Chiltepin variety, and one CDPK present in CM334 was lost in Chiltepin. The majority of CDPK and CRK genes were expressed in different pepper tissues and developmental stages, and 10, 12, and 8 CDPK genes were transcriptionally modified by salt, heat, and Ralstonia solanacearum stresses, respectively. Furthermore, these genes were found to respond specifically to one stress as well as respond synergistically to two stresses or three stresses, suggesting that these CDPK genes might be involved in the specific or synergistic response of pepper to salt, heat, and R. solanacearum. Our results lay the foundation for future functional characterization of pepper CDPK and its closely related gene families.

No MeSH data available.


Related in: MedlinePlus