钩藤CCD基因家族全基因组鉴定及表达模式分析

[24] Kulkarni K P, Vishwakarma C, Sahoo S P, et al. A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice [J]. Journal of Genetics. 2014, 93 (2): 389-401.Whole Genome Identification and Expression Pattern of CCD Gene Family in Uncaria rhynchophylla

关键词:  钩藤  类胡萝卜素裂解双加氧酶  基因家族  基因表达

Key words:  Uncaria rhynchophylla  carotenoid cleavage dioxygenase  gene family  gene expression

摘要:

【目的】为了解钩藤（Uncaria rhynchophylla）Carotenoid Cleavage Dixoygenases （CCD）基因家族的表达特性及其在分枝调控中的潜在作用，对钩藤CCD基因家族进行全基因组鉴定及表达模式分析。【方法】基于拟南芥CCD基因家族序列信息在钩藤全基因组内筛选并鉴定钩藤CCD基因家族成员，并对其进行系统进化、蛋白理化性质、功能结构、保守基序及启动子顺式作用元件等分析，再结合转录组数据进行UrCCD基因在不同组织中的表达模式分析。【结果】（1）鉴定出20个UrCCD基因，其中18个精准定位在8条染色体上，系统进化分析将17个UrCCD基因分类为2个大类别（CCD和NCED），共计7个亚家族（CCD1、CCD4、CCD7、CCD8、NCED3、NCED6、NCED9），所鉴定出的成员均具备典型的RPE65型蛋白结构域。（2）其启动子区域有与逆境胁迫、激素响应以及生长发育等生物过程密切相关的顺式作用元件。（3）转录组数据分析表明UrCCD4-b、UrCCD1-c基因在钩藤的叶组织中具有显著的高表达，UrCCD7-b、UrCCD8-a在根、茎的表达较高；与二叉植株相比，UrCCD1-b、UrCCD8-a、UrCCD8-b在三叉植株中茎节中的表达量显著下调。【结论】钩藤CCD基因家族成员具有明显的组织表达特异性，UrCCD1-b、UrCCD8-a、UrCCD8-b在钩藤分枝调控方面具有重要潜在作用，以上研究结果为进一步研究钩藤CCD基因家族的功能奠定了一定的基础。

Abstract:

【Objective】: To understand the expression characteristics of the Carotenoid Cleavage Dixoygenases (CCD) gene family in Uncaria rhynchophylla and its potential role in branching regulation, a genome-wide identification and expression pattern analysis of the CCD gene family in U. rhynchophylla were carried out. 【Methods】: Based on the sequence information of the CCD gene family in Arabidopsis thaliana, the members of the CCD gene family in U. rhynchophylla were screened and identified within the whole genome of U. rhynchophylla. Then, phylogenetic analysis, physicochemical properties of proteins, functional structures, conserved motifs, and cis-acting elements in the promoter region were performed. Combined with the transcriptome data, the expression patterns of UrCCD genes in different tissues were analyzed. 【Results】: (1) Twenty UrCCD genes were identified, among which 18 were precisely located on 8 chromosomes. Phylogenetic analysis classified 17 UrCCD genes into two major categories (CCD and NCED), a total of seven subfamilies (CCD1, CCD4, CCD7, CCD8, NCED3, NCED6, NCED9). All the identified members possessed the typical RPE65-type protein domain. (2) There were cis-acting elements closely related to biological processes such as stress responses, hormone responses, and growth and development in the promoter region. (3) Transcriptome data analysis showed that UrCCD4-b and UrCCD1-c genes had significantly high expression in the leaf tissues of U. rhynchophylla, and UrCCD7-b and UrCCD8-a had higher expression in roots and stems. Compared with the bifurcated plants, the expression levels of UrCCD1-b, UrCCD8-a, and UrCCD8-b in the stem nodes of the trifurcated plants were significantly down-regulated. 【Conclusion】: The members of the CCD gene family in U. rhynchophylla have obvious tissue expression specificity. UrCCD1-b, UrCCD8-a, and UrCCD8-b play important potential roles in the branching regulation of U. rhynchophylla. The above research results lay a certain foundation for further studying the functions of the CCD gene family in U. rhynchophylla.