木荷WRKY基因家族的全基因组鉴定与分析
Genome-Wide Identification and Analysis of the WRKY Gene Family in Schima superba
[目的]基于木荷基因组数据，利用生物信息学手段，鉴定木荷WRKY基因家族所有成员，并对其理化性质、系统进化、顺式作用元件、基因结构、基序分析、保守结构域、染色体定位以及共线性进行分析，为后续探究SsWRKY基因功能作用提供参考。[方法]采用生物信息学方法，基于木荷基因组数据对木荷WRKY基因家族进行鉴定，通过TBtoool软件对该家族进行理化性质、基因结构、保守结构域、染色体定位、共线性分析分析。利用MEGA软件构建系统发育树，PlantCARE网站对顺势作用元件分析。[结果]在木荷基因组数据中共鉴定出 82个WRKY基因家族成员，并根据相似性命名为SsWRKY1—SsWRKY75，不均匀分布在 18 条染色体上，编码氨基酸个数在 153-770，分子量 17701-783888.06 Da，有 30 个SsWRKY为碱性蛋白(pI＞7)，酸性蛋白52个(pI＜7)，且有 80 个为不稳定蛋白。基于系统进化关系将其划分为3大类群(Ⅰ-Ⅲ)，第Ⅱ类群又被分成5个亚群(Ⅱa-e)，Ⅱ组成员最多。SsWRKY基因的外显子数量为 2～7 个，内含子数量为 1～6个，同一类家族中的结构域及保守基序相似，所有成员都含有WRKYGQK七肽保守结构域和锌指结构。木荷WRKY基因家族中片段重复在基因家族扩展中发挥的作用大于串联重复，且木荷与拟南芥的共线性关系远高于水稻。分析启动子发现，存在多种植物生长发育、激素、干旱、低温等响应元件。[结论]在木荷中共鉴定出82个 WRKY 家族基因，分为 7 个亚族，不同亚族间的基因结构和蛋白保守结构域有所不同，片段重复可能是进化驱动力，以上结果为开展木荷WRKY基因功能进一步研究其生物学功能提供了有价值的线索。
[Objective]Based on the genome data of Schima superba,bioinformatics methods were used to identify all members of the WRKY gene family in Schima superba.Analyses were conducted on their physicochemical properties,phylogeny,cis-acting elements,gene structure,motif analysis,conserved domains,chromosomal localization,and collinearity.This provides a reference for subsequent exploration of the functional roles of SsWRKY genes.[Method]Using bioinformatics methods,the WRKY gene family in Schima superba was identified based on its genome data.The physicochemical properties,gene structure,conserved domains,chromosomal localization,and collinearity of this family were analyzed using TBtools software.Phylogenetic trees were constructed using MEGA software,and cis-acting elements were analyzed using the PlantCARE website.[Result]A total of 82 members of the WRKY gene family were identified in the Schima superba genome data and named SsWRKY1 to SsWRKY75 based on their similarity.These genes are unevenly distributed across 18 chromosomes,encoding amino acids ranging from 153 to 770,with molecular weights between 17,701 and 783,888.06 Da.Among them,30 SsWRKY proteins are basic(pI>7),52 are acidic(pI<7),and 80 are unstable proteins.Based on phylogenetic relationships,they were divided into three major groups(I-III),with group II further subdivided into five subgroups(IIa-e),and group II having the most members.The number of exons in SsWRKY genes ranges from 2 to 7,and the number of introns ranges from 1 to 6.The domains and conserved motifs within the same family are similar,and all members contain the WRKYGQK heptapeptide conserved domain and zinc finger structure.In the SsWRKY gene family,segmental duplication plays a more significant role in gene family expansion than tandem duplication,and the collinearity relationship between Schima superba and Arabidopsis thaliana is much higher than that with Oryza sativa.Promoter analysis revealed the presence of various response elements related to plant growth and development,hormones,drought,and low temperature.[Conclusion]We identified a total of 82 WRKY family genes were identified in Schima superba,which are divided into 7 subfamilies.The gene structures and conserved protein domains differ among the various subfamilies.Segmental duplication may be a driving force in their evolution.These results provide valuable clues for further research into the biological functions of WRKY genes in Schima superba.
陈昌娅;蔡燕灵;何波祥;张谦;梁东成;汪迎利;尧俊;
广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;广东省林业科学研究院,广东 广州 510520;
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