Articles
Identification and analysis of the CCD gene family in Chinese jujube (Ziziphus jujuba Mill.)
Article number
1350_19
Pages
161 – 170
Language
English
Abstract
In order to analyze the CCD (carotenoid cleavage dioxygenase) gene family and further study its function, a total of 13 ZjCCD members were identified by bioinformatics method, and the physical and chemical properties, gene structure, promoter elements, chromosome location and expression pattern were analyzed.
The results showed that all the 13 ZjCCD genes identified contained RPE65 conserved domain.
The length of the amino acid sequence encoding the protein was between 123 aa~611 aa, the molecular weight was between 13.58~68.79 kDa.
The results of subcellular localization prediction showed that ZjCCD family members were mainly located in cytoplasmic.
Secondary structure analysis showed that the proportion of random coil was the highest and performs the primary function.
Phylogenetic tree analysis divided the ZjCCD gene family into five subfamilies (CCD1, CCD4, CCD7, CCD8, and NCED). The NCED subfamily is divided into NCED3 and NCED6 subgroups.
The gene structure of ZjCCD4 and ZjNCED family members was simple with only one exon.
The gene structure of the members in the same subfamily is similar.
It is predicted that motif3 only exists in ZjCCD1. Promoter analysis showed that ZjCCD genes might be regulated by many factors such as light, anaerobic induction and abscisic acid. ZjNCED3a and ZjCCD4 of 13 ZjCCD genes were not located on 12 chromosomes of Ziziphus jujuba. The other 11 members were located on 4 chromosomes of Chr1, Chr5, Chr6 and Chr7, at the same time, 4 pairs of genes were found to have gene duplication events. ZjCCD1a, ZjCCD1d and ZjCCD4 were highly expressed during fruit development, and there was obvious regularity in the expression pattern of CCD gene.
It is suggested that these three genes may be related to the synthesis of aroma and color formation.
This study can lay a theoretical foundation for the functional study of ZjCCD genes.
The results showed that all the 13 ZjCCD genes identified contained RPE65 conserved domain.
The length of the amino acid sequence encoding the protein was between 123 aa~611 aa, the molecular weight was between 13.58~68.79 kDa.
The results of subcellular localization prediction showed that ZjCCD family members were mainly located in cytoplasmic.
Secondary structure analysis showed that the proportion of random coil was the highest and performs the primary function.
Phylogenetic tree analysis divided the ZjCCD gene family into five subfamilies (CCD1, CCD4, CCD7, CCD8, and NCED). The NCED subfamily is divided into NCED3 and NCED6 subgroups.
The gene structure of ZjCCD4 and ZjNCED family members was simple with only one exon.
The gene structure of the members in the same subfamily is similar.
It is predicted that motif3 only exists in ZjCCD1. Promoter analysis showed that ZjCCD genes might be regulated by many factors such as light, anaerobic induction and abscisic acid. ZjNCED3a and ZjCCD4 of 13 ZjCCD genes were not located on 12 chromosomes of Ziziphus jujuba. The other 11 members were located on 4 chromosomes of Chr1, Chr5, Chr6 and Chr7, at the same time, 4 pairs of genes were found to have gene duplication events. ZjCCD1a, ZjCCD1d and ZjCCD4 were highly expressed during fruit development, and there was obvious regularity in the expression pattern of CCD gene.
It is suggested that these three genes may be related to the synthesis of aroma and color formation.
This study can lay a theoretical foundation for the functional study of ZjCCD genes.
Publication
Authors
X.F. Xue, A.L. Zhao, Y.K. Wang, H.Y. Ren, D.K. Li, Y. Li, W.L. Su
Keywords
Ziziphus jujube, CCD gene family, bioinformatics, phylogenetic analysis, expression analysis
Groups involved
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