Genome-wide identification, phylogenetic relationships, and expression analysis of the carotenoid cleavage oxygenase gene family in pepper.
Carotenoid cleavage oxygenases (CCOs) are a family of dioxygenases, which specifically catalyze the cleavage of conjugated double bonds in carotenoids and apocarotenoids in plants. In this study, genome-wide analysis of CCO genes in pepper plants was performed using bioinformatic methods. At least 11 members of the CCO gene family were identified in the pepper genome. Phylogenetic analysis showed that pepper and tomato CCO genes could be divided into two groups (CCDs and NCEDs). The CCD group included five sub-groups (CCD1, CCD4, CCD7, CCD8, and CCD-like). These results indicate that there is a close genetic relationship between the two species. Sequence analysis using the online tool, Multiple Expectation Maximization for Motif Elicitation (MEME), showed that the CCO proteins comprise multiple conserved motifs, with 20 to 41 amino acids. In addition, multiple cis-acting elements in the promoter of CCO genes were identified using the online tool PlantCARE, and were found to be involved in light responsiveness, plant hormone regulation, and biotic and abiotic stresses, suggesting potential roles of these proteins under different conditions. RNA-seq analysis revealed that the CCO genes exhibit distinct patterns of expression in the roots, stems, leaves, and fruit. These findings suggest that the CCO genes have important roles in the vegetative and reproductive development of pepper plants.
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
X H
XH
Zhang
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
H Q
HQ
Liu
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
Q W
QW
Guo
Zhejiang Mariculture Research Institute, Wenzhou, China.
C F
CF
Zheng
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
C S
CS
Li
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
X M
XM
Xiang
Quzhou Academy of Agricultural Sciences, Quzhou, Zhejiang, China.
D F
DF
Zhao
Wulanchabu Academy of Agricultural Sciences, Wulanchabu, Inner Mongolia, China.
J
J
Liu
Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
J
J
Luo
College of Agricultural, Yunnan University, Kunming, Yunnan, China.
D K
DK
Zhao
Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, Zhejiang, China.
J Q
JQ
Zheng
State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China wanhongjian@sina.com.
H J
HJ
Wan
D020816:Amino Acid Motifs; D002212:Capsicum / Q000201:enzymology* / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D007438:Introns / Q000235:genetics; D018551:Solanum lycopersicum / Q000201:enzymology / Q000235:genetics; D005810:Multigene Family; D010105:Oxygenases / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
D010105:Oxygenases; C500451:carotenoid oxygenase