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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

Phylogenetic tree of CDPK and CRK genes from genomes of pepper and Arabidopsis. A neighbor-joining tree was constructed using the MEGA5.0 program with 1000 bootstrap analyses using the full length amino acid sequences of 31 pepper CDPK genes, five pepper CRK genes, 34 Arabidopsis CDPK genes, and eight Arabidopsis CRK genes. The CDPK genes were classified into four subfamilies (groups I, II, III, and IV). The CRK genes were classified into two subfamilies (CRK I and CRK II).
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Figure 2: Phylogenetic tree of CDPK and CRK genes from genomes of pepper and Arabidopsis. A neighbor-joining tree was constructed using the MEGA5.0 program with 1000 bootstrap analyses using the full length amino acid sequences of 31 pepper CDPK genes, five pepper CRK genes, 34 Arabidopsis CDPK genes, and eight Arabidopsis CRK genes. The CDPK genes were classified into four subfamilies (groups I, II, III, and IV). The CRK genes were classified into two subfamilies (CRK I and CRK II).

Mentions: To examine the phylogenetic relationship among the CDPKs and CRKs in pepper, the CDPKs of Arabidopsis and pepper, were constructed from alignments of the full-length kinase sequences using MEGA5.0. Similar to the previous studies in Arabidopsis, CDPK genes in pepper were grouped into four subfamilies, with 12, eight, seven, and two members in subfamily I, II, III, and IV, respectively (Figure 2 and Table 2). Similar to the CDPKs in Arabidopsis, Populus, rice, and cotton, subfamilies I and II in pepper consist of large numbers of CDPKs, which exhibit a great diversity in number among different plant species: for example, four more CDPKs in subfamily I were found in cotton than in Arabidopsis, and seven more CDPKs in subfamily II were found in cotton than in poplar and rice. The members in subfamily III and IV were approximately identical across the five plant species, and subfamily IV contained the lowest number of CDPKs. Five CRKs were found in rice and pepper, whereas in Arabidopsis and Populus trichocarpa, eight and nine CRKs were found, respectively. These results indicated that differences in the number of CDPK genes in different plant species might be contributed largely by the numbers of CDPK I or CDPK II that have evolved independently among the different organisms.


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)

Phylogenetic tree of CDPK and CRK genes from genomes of pepper and Arabidopsis. A neighbor-joining tree was constructed using the MEGA5.0 program with 1000 bootstrap analyses using the full length amino acid sequences of 31 pepper CDPK genes, five pepper CRK genes, 34 Arabidopsis CDPK genes, and eight Arabidopsis CRK genes. The CDPK genes were classified into four subfamilies (groups I, II, III, and IV). The CRK genes were classified into two subfamilies (CRK I and CRK II).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Phylogenetic tree of CDPK and CRK genes from genomes of pepper and Arabidopsis. A neighbor-joining tree was constructed using the MEGA5.0 program with 1000 bootstrap analyses using the full length amino acid sequences of 31 pepper CDPK genes, five pepper CRK genes, 34 Arabidopsis CDPK genes, and eight Arabidopsis CRK genes. The CDPK genes were classified into four subfamilies (groups I, II, III, and IV). The CRK genes were classified into two subfamilies (CRK I and CRK II).
Mentions: To examine the phylogenetic relationship among the CDPKs and CRKs in pepper, the CDPKs of Arabidopsis and pepper, were constructed from alignments of the full-length kinase sequences using MEGA5.0. Similar to the previous studies in Arabidopsis, CDPK genes in pepper were grouped into four subfamilies, with 12, eight, seven, and two members in subfamily I, II, III, and IV, respectively (Figure 2 and Table 2). Similar to the CDPKs in Arabidopsis, Populus, rice, and cotton, subfamilies I and II in pepper consist of large numbers of CDPKs, which exhibit a great diversity in number among different plant species: for example, four more CDPKs in subfamily I were found in cotton than in Arabidopsis, and seven more CDPKs in subfamily II were found in cotton than in poplar and rice. The members in subfamily III and IV were approximately identical across the five plant species, and subfamily IV contained the lowest number of CDPKs. Five CRKs were found in rice and pepper, whereas in Arabidopsis and Populus trichocarpa, eight and nine CRKs were found, respectively. These results indicated that differences in the number of CDPK genes in different plant species might be contributed largely by the numbers of CDPK I or CDPK II that have evolved independently among the different organisms.

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