杜仲miR172基因家族的生物信息学分析与功能预测

Bioinformatics analysis and function prediction of miR172 gene family in Eucommia ulmoides

为了解杜仲miR172家族成员的进化特征及其在杜仲生长发育过程中的作用。从杜仲小RNA高通量测序结果(登录号:SRP216820)及已发表文献中获取杜仲miR172家族前体和成熟体序列,进行序列比对、WebLogo保守性分析、系统发育树构建、前体茎环结构预测、启动子结构分析、靶基因预测及功能预测。结果表明,杜仲miR172家族共有8条前体和8条成熟体序列,且前体序列均能形成稳定的茎环结构;序列比对和WebLogo分析表明,除eu-miR172d-5p以外的其他7个成员的成熟体序列保守性较高,但前体序列的保守性均较低;进化分析表明,该家族成熟体进化高度保守,而前体的进化保守性较低;启动子分析表明,杜仲miR172家族启动子包含丰富的光反应原件及激素响应元件和胁迫响应元件,说明其可能调控杜仲的花器官形成和发育及逆境胁迫响应等过程;靶基因预测表明,杜仲miR172家族的靶基因数目较多,其靶基因参与杜仲的生长发育和逆境胁迫等过程,该小RNA家族成员主要调控AP2基因的表达。表明杜仲miR172家族成员在进化过程中既保守又有一定分化,其主要通过调控AP2基因的表达在杜仲生长发育过程中发挥重要调控作用。

To understand the evolutionary characteristics of the miR172 family members and their role in the growth and development of Eucommia ulmoides,the precursor and mature sequences of miR172 family were collected from the high-throughput sequencing results(accession number:SRP216820)and published literature related to E.ulmoides.In addition,sequence alignment,WebLogo conservation analysis,phylogenetic tree construction,precursor stem-loop structure prediction,promoter structure analysis,target gene prediction and functional prediction were performed.The E.ulmoides miR172 family contains 8 precursor sequences and 8 mature sequences,and all precursor sequences can form a stable stem-loop structure.Sequence alignment and WebLogo analysis showed that 7 mature sequences(except eu-miR172d-5p)were highly conservative,however the precursor sequences were less conservative.Evolutionary analysis showed that the mature sequences of this family were highly conservative,but the precursor sequences were less conservative.Promoter analysis showed that the E.ulmoides miR172 family promoters contained abundant photoreaction components and hormone response elements and stress response elements,indicating that they may regulate the process of flower organ formation and stress response.Target gene prediction showed that there were many target genes for miR172 family of E.ulmoides,and they were involved in E.ulmoides growth and development and adversity stress,but the miR172 family members mainly regulated the expression of AP2 genes.The E.ulmoides miR172 family members were both conservative and differentiated during evolution,and they play an important regulatory roles in the growth and development of E.ulmoides by regulating AP2 expression.