薄壳山核桃全基因组LBD基因家族的生物信息学分析  

Genome-wide identification and bioinformatics analysis of LBD family of transcription factors in Carya illinoensis

作　　者：黄元城 郭文磊[1] 王正加[1] HUANG Yuancheng;GUO Wenlei;WANG Zhengjia(State Key Laboratory of Subtropical Silviculture,Zhejiang A&F University,Hangzhou 311300,Zhejiang,China)

机构地区：[1]浙江农林大学亚热带森林培育国家重点实验室,浙江杭州311300

出　　处：《浙江农林大学学报》2021年第3期464-475,共12页Journal of Zhejiang A&F University

基　　金：浙江省科技厅重大研发专项(2018C02004);浙江省农业新品种选育重大科技专项(2016C02052-13);“十三五”国家重点研发计划项目(2018YFD1000604)。

摘　　要：【目的】研究薄壳山核桃Carya illinoensis LBD基因家族结构特征、进化模式和在胚发育过程中的表达模式。【方法】运用生物信息学手段鉴定薄壳山核桃LBD基因,分析该基因结构特征、系统发生学关系、显花植物中的进化历史和在胚发育过程中3个关键阶段的表达模式。【结果】薄壳山核桃全基因组中一共鉴定到52个候选LBD基因。根据基因结构、系统发生学最大似然树和Motif分析可分为3类:GroupⅠ、GroupⅡ和GroupⅢ。多序列比对分析中,52个LBD基因LOB结构域中鉴定出3个重要的结构:CX2CX6CX3C锌指结构、高度保守的甘氨酸GAS结构和亮氨酸拉链(zipper-like)结构,并且在3类内都分别发生了特异性的的变异或者缺失。根据代表性显花植物LBD基因家族的系统发生学分析,从变异程度看GroupⅠ和GroupⅡ相对较为保守,而GroupⅢ内的所有LBD基因共享1支较长的分支,它们已发生了较大的变异,可能已经分化出新的功能。表达分析结果显示:LBD基因家族参与调控胚发育过程,通常控制子叶的发育和形态建成。薄壳山核桃LBD基因中又有在整个胚发育过程中都高表达的一簇基因,这些基因可能在胚发育过程中发挥了更加重要的作用。【结论】薄壳山核桃全基因组中共获得LBD基因52个,共可分为3个亚家族,不同的亚家族具有不同的基因结构、蛋白质结构、进化模式和表达模式,转录组表达分析显示:不同亚家族之间在胚发育不同阶段具有差异性表达,它们共同参与调控薄壳山核桃胚发育过程。[Objective] This study is aimed to investigate the structural features and the evolutionary patterns of the LBD transcription factor family as well as their expression patterns throughout the embryonic development in Carya illinoensis. [Method] With bioinformatic software employed, efforts were made to identify the LBD gene and analyze its gene structure characteristics, phylogeny relationships and evolutionary history in flower plants, as well as their expression patterns at the three key stages througout the embryonic development.[Result] Within the whole genome in C. illinoensis there were a total of 52 candidate LBD genes which, in terms of gene structure, maximum likelihood phylogenetic tree and motif analysis, could be classified into 3 categories: Group Ⅰ, Group Ⅱ and Group Ⅲ. After the multiple sequences alignment analysis three important structures in the LOB domains of 52 LBD genes were identified, namely the CX2 CX6 CX3 C zinc finger structure, the highly conserved glycine GAS structure and the leucine zipper-like structure with the occurrenceof specific mutations or deletions in each of them. According to the LBD gene family phylogenetic analysis of representative flowering plants, Group Ⅰ and Group Ⅱ are relatively conservative, while all LBD genes in Group Ⅲ share a longer branch which indicates that they have undergone greater variation and new functions have been differentiated. The expression analysis showed that the LBD gene family participates in the function of regulating the development of embryos, usually with control over the development and morphogenesis of cotyledons and there is a cluster of genes in the LBD gene of hickory pecans that are highly expressed during the entire embryo development process playing a highly significant role. [Conclusion] A total of 52 LBD genes were obtained in the whole genome of C. illinoensis, which can be divided into three different subfamilies with different gene structures, protein structures, evolutionary patterns, and expression patterns, a

关 键 词：薄壳山核桃 LBD 转录因子 系统进化 基因功能 

分 类 号：S722.3[农业科学—林木遗传育种] Q75[农业科学—林学]