Table_1_Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera.pdf

IntroductionLignin is a complex aromatic polymer plays major biological roles in maintaining the structure of plants and in defending them against biotic and abiotic stresses. Cinnamoyl-CoA reductase (CCR) is the first enzyme in the lignin-specific biosynthetic pathway, catalyzing the conversion of hydroxycinnamoyl-CoA into hydroxy cinnamaldehyde. Dalbergia odorifera T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the CCR family genes in D. odorifera have not been identified, and their function in lignin biosynthesis remain uncertain.Methods and ResultsHere, a total of 24 genes, with their complete domains were identified. Detailed sequence characterization and multiple sequence alignment revealed that the DoCCR protein sequences were relatively conserved. They were divided into three subfamilies and were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that seven DoCCRs were grouped together with functionally characterized CCRs of dicotyledons involved in developmental lignification. Synteny analysis showed that segmental and tandem duplications were crucial in the expansion of CCR family in D. odorifera, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of DoCCRs were mainly associated with stress, light, hormones, and growth/development. Further, analysis of expression profiles from the RNA-seq data showed distinct expression patterns of DoCCRs among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 DoCCRs, located in the intron or untranslated regions (UTRs), and mononucleotide predominated. A pair of primers with high polymorphism and good interspecific generality was successfully developed from these SSRs, and 7 alleles were amplified in 105 wild D. odorifera trees from 17 areas covering its whole native distribution.DiscussionOverall, this study provides a basis for further functional dissection of CCR gene families, as well as breeding improvement for wood properties and stress resistance in D. odorifera.

引言：木质素是一种复杂的芳香族聚合物，在维持植物结构及抵御生物和非生物胁迫方面发挥着至关重要的生物学作用。肉桂酰辅酶A还原酶（CCR）是木质素特异性生物合成途径中的首步酶，催化将羟基肉桂酰辅酶A转化为羟基肉桂醛。T. Chen所描述的香枝木（Dalbergia odorifera）是一种珍稀的玫瑰木树种，适用于家具、工艺品和医药。然而，香枝木中的CCR家族基因尚未被鉴定，其在木质素生物合成中的功能尚不明确。
方法与结果：本研究共鉴定了24个基因及其完整结构域。详细的序列特征描述和多重序列比对揭示了DoCCR蛋白序列相对保守。这些序列被分为三个亚家族，并均匀分布在10条染色体上。系统发育分析表明，七个DoCCRs与功能已知的涉及发育木质化的双子叶植物CCRs聚为一组。同源分析显示，片段化和串联重复在香枝木CCR家族的扩张中至关重要，而净化选择成为推动这些基因进化的主要力量。DoCCR推测启动子区域中的顺式作用元件主要与胁迫、光照、激素以及生长/发育相关。此外，对RNA-seq数据的表达谱分析显示，DoCCRs在不同组织和器官中以及响应茎部受伤时表现出独特的表达模式。另外，在19个DoCCR中鉴定到74个简单序列重复（SSRs），这些SSRs位于内含子或不翻译区（UTRs）中，以单核苷酸为主。从这些SSRs中成功开发出一对高多态性和良好种间通用性的引物，并在覆盖其整个原生分布区域的105株野生香枝木树中扩增出7个等位基因。
讨论：总体而言，本研究为CCR基因家族的进一步功能解析以及香枝木木材特性和抗逆性的育种改良提供了基础。