荆芥HD-Zip基因家族的全基因组鉴定及分析

Genome-wide identification and expression analysis of HD-Zip gene family in Schizonepeta tenuifolia

【目的】鉴定荆芥Schizonepeta tenuifolia的HD-Zip基因家族,利用生物信息学方法分析其在全基因组中的分布和相关特征以及在不同时期中的表达规律,为该家族基因的进一步研究奠定基础。【方法】根据已经表征的HD-Zip基因,筛选荆芥基因组内的HD-Zip基因序列,利用MEME、PlantCARE、NCBI、MEGA X、MCScanX、Circos等在线网站及软件对蛋白序列进行基本理化性质分析、进化树构建、染色体定位、基因结构分析、共线性基因分析等。【结果】在荆芥全基因组中共鉴定到42条HD-Zip基因序列,它们可被分为4个亚家族,分别含有16、7、5、14个基因,亚家族之间的基因长度、结构及保守基序差异显著,但在亚家族内部保守,荆芥基因组与拟南芥Arabidopsis thaliana基因组共线性分析发现有37对基因,可能具有相似的生物学功能。荆芥的4个亚家族基因的顺式元件中均高频出现了光响应、脱落酸响应、MeJA响应等元件,在不同生长时期的叶片及部位的转录组数据中具有不同的表达趋势,Ⅰ亚家族主要在幼叶中表达,Ⅱ和Ⅲ亚家族主要在根中在表达,Ⅳ亚家族主要在叶中表达。【结论】在荆芥基因组中共获得42条HDZip基因序列,被分为4个亚家族(HD-ZipⅠ~Ⅳ),亚家族内部高度保守,亚家族之间差异显著,其基因结构、保守结构域及表达模式不同。亚家族Ⅰ和Ⅱ,亚家族Ⅲ和Ⅳ亲缘关系更近,HD-Zip基因具有组织表达差异性,协同调控了荆芥的生长发育和次生代谢。

[Objective]This study,with the identification of the HD-Zip gene family in Schizonepeta tenuifolia and an bioinformatic analysis of its distribution and related characteristics in the whole genome and expression pattern in different stages,is aimed to provide a basis for further study of this gene family.[Method]Genes in the genome were first screened in accordance with the characterized HD-Zip genes before MEME,Plant CARE,NCBI,MEGA X,MCScanX and Circos were used for the analysis of the basic properties of protein sequences,the construction of Maximum Likeliood(ML)tree,mapping of chromosomes and the analysis of gene structure and colinear gene respectively.[Result](1)A total of 42 HD-Zip genes were identified and they could be divided into four subgroups(Ⅰ−Ⅳ),containing 16,7,5,14 genes respectively.(2)The gene length,structure and Motif of the subgroups varied significantly from each though relatively reserved with in each of them.(3)The collinear analysis of the genome of S.tenuifolia and Arabidopsis thaliana showed that 37 pairs of genes may have similar biological functions with light response,abscisic acid response and MeJA response found in ciselements of 4 subfamily genes promoters of S.tenuifolia,showing different expression profiles in the transcriptome data of different growth stages of leaves and different parts.(4)The HD-ZipⅠwas mainly expressed in young leaves,HD-ZipⅡandⅢwere mainly expressed in roots whereas HD-ZipⅣwas mainly expressed in leaves.[Conclusion]The total 42 HD-Zip genes obtained from S.tenuifolia genome were divided into 4 subgroups(Ⅰ−Ⅳ)with highly conserved genes and significant differences among subgroups with their gene structure,motif,and expression pattern being different.HD-ZipⅠandⅡ,and HD-ZipⅢandⅣare more closely related to each other with HD-Zip genes expressed specifically indifferent tissues and synergistically regulating the growth,development and secondary metabolism of S.tenuifolia.The results of this study provide a bioinformatic reference for the further study of this family’s biological functions.