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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

Hierarchical clustering analyses of the expression of pepper CDPK and CRK genes in different pepper tissues. The microarray data were obtained from pepper gene expression database under the series accession number (Kim et al., 2014b). PC, PL, and B indicate the pericarp, placenta, and breaker stages. DPA, days post-anthesis, CM, CM334 plants, MG, Mature Green. B, Break. B10, 10 days post-anthesis, respectively.
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Figure 4: Hierarchical clustering analyses of the expression of pepper CDPK and CRK genes in different pepper tissues. The microarray data were obtained from pepper gene expression database under the series accession number (Kim et al., 2014b). PC, PL, and B indicate the pericarp, placenta, and breaker stages. DPA, days post-anthesis, CM, CM334 plants, MG, Mature Green. B, Break. B10, 10 days post-anthesis, respectively.

Mentions: Extensive studies have suggested a close relationship between gene expression and function. To investigate the possible roles of the CDPK genes in the pepper genome, the expression profiles of the 36 CDPK and CRK genes were analyzed in 17 tissues and developmental stages using microarray expression data recently published by Kim et al from CM334 pepper plants (Figure 4, Kim et al., 2014b). The results showed that most of the CDPK and CRK genes were expressed in different tissues and developmental stages in pepper. In addition, we analyzed the expression of all the pepper CDPK and CRK genes in different organs such as root, stem, leaf, flower, and fruit in plants of GZ03, an inbred line of pepper, under normal conditions using qRT-PCR (Figure 5). All of the CDPK genes except CaCDPK16, and all of CRK genes in the pepper genome, were expressed in at least one of the five tissues in non-stressed pepper plants, whereas CaCDPK16 was not expressed in any of the five organs in non-stressed pepper plants. CaCDPK22 was expressed constitutively in roots, but its expression levels in other organs were very low. CaCDPK2, CaCDPK3, CaCDPK4, and CaCDPK31 were expressed constitutively only in flowers. All these data indicate that the members of the CDPK gene family and CRK genes might be involved in the growth and development of different tissues or organs of pepper plants.


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)

Hierarchical clustering analyses of the expression of pepper CDPK and CRK genes in different pepper tissues. The microarray data were obtained from pepper gene expression database under the series accession number (Kim et al., 2014b). PC, PL, and B indicate the pericarp, placenta, and breaker stages. DPA, days post-anthesis, CM, CM334 plants, MG, Mature Green. B, Break. B10, 10 days post-anthesis, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Hierarchical clustering analyses of the expression of pepper CDPK and CRK genes in different pepper tissues. The microarray data were obtained from pepper gene expression database under the series accession number (Kim et al., 2014b). PC, PL, and B indicate the pericarp, placenta, and breaker stages. DPA, days post-anthesis, CM, CM334 plants, MG, Mature Green. B, Break. B10, 10 days post-anthesis, respectively.
Mentions: Extensive studies have suggested a close relationship between gene expression and function. To investigate the possible roles of the CDPK genes in the pepper genome, the expression profiles of the 36 CDPK and CRK genes were analyzed in 17 tissues and developmental stages using microarray expression data recently published by Kim et al from CM334 pepper plants (Figure 4, Kim et al., 2014b). The results showed that most of the CDPK and CRK genes were expressed in different tissues and developmental stages in pepper. In addition, we analyzed the expression of all the pepper CDPK and CRK genes in different organs such as root, stem, leaf, flower, and fruit in plants of GZ03, an inbred line of pepper, under normal conditions using qRT-PCR (Figure 5). All of the CDPK genes except CaCDPK16, and all of CRK genes in the pepper genome, were expressed in at least one of the five tissues in non-stressed pepper plants, whereas CaCDPK16 was not expressed in any of the five organs in non-stressed pepper plants. CaCDPK22 was expressed constitutively in roots, but its expression levels in other organs were very low. CaCDPK2, CaCDPK3, CaCDPK4, and CaCDPK31 were expressed constitutively only in flowers. All these data indicate that the members of the CDPK gene family and CRK genes might be involved in the growth and development of different tissues or organs of pepper plants.

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