鹰嘴豆miRNA中miR156家族的生物信息学分析及靶基因预测

Bioinformatics Analysis of miR156 Family in Chickpea miRNA and Prediction of Their Target Genes

为了揭示鹰嘴豆Car-miR156基因家族的进化过程和表达模式,对Car-miR156家族8个成员的序列进行生物信息学分析及靶基因预测。染色体定位结果表明7个Car-miR156基因定位在鹰嘴豆Ca4、Ca5、Ca6和Ca7四条染色体上,而Car-miR156g定位在scaffold1580上。序列比对发现8个Car-miR156基因的成熟序列具有高度一致性,仅在5'端第1、14和15个碱基存在差异。二级结构分析结果表明,8个Car-miR156成员的前体序列都能形成稳定的茎环结构,Car-miR156h成熟的miRNA序列位于3'端,Car-miR156a/b/c/d/e/f/g成熟的miRNA序列位于5'端。此外,Car-miR156a/d/f/g与大豆的miR156家族成员亲缘关系较近,Car-miR156e与拟南芥Ath-miR156j聚在一个分支,而Car-miR156b单独为一个分支。靶基因预测表明SQUAMOSA启动子结合蛋白家族成员(SPL2/3/6/7/9/13A)是Car-miR156的靶基因,Car-miR156a/c/d/e/f/g/h还能够靶向调控大刍草颖片架构1类基因。转录组数据分析表明,Car-miR156a/c/d/f在鹰嘴豆8个组织中都有表达,Car-miR156b在根中不表达,Car-miR156e在茎和花中不表达。这些研究结果为研究鹰嘴豆Car-miR156家族成员的表达及其靶基因的功能提供了基础。

To reveal the evolution and expression patterns of the Car-miR156 gene family in chickpea,bioinformatics analysis and target gene prediction were performed on the sequences of eight members of the Car-miR156 family.Chromosomal mapping results showed that seven Car-miR156 genes were located on the four chromosomes of Ca2,Ca5,Ca6 and Ca7,while Car-miR156g was located on scaffold1580.Sequence alignments revealed that the mature sequences of the eight Car-miR156 genes were high identity,with differences only at the 1st,14th and 15th bases at the 5'end.The secondary structure analysis results showed that the precursor sequences of the eight Car-miR156 members could form a stable stem-loop structure,and the mature miRNA sequence of Car-miR156h was located at the 3'end,the mature miRNA sequence of Car-miR156a/b/c/d/e/f/g is located at the 5'end.In addition,Car-miR156a/c/d/f/g were closely related to soybean miR156.Car-miR156e and Ath-miR156j were clustered in one branch,while Car-miR156b was clustered in a single branch.Target gene prediction indicated that the target gene of the Car-miR156 family members was members of the SQUAMOSA promoter binding protein family(SPL2/3/6/7/9/13A),Car-miR156a/c/d/e/f/g/h was also able to target and regulate the teosinte glume architecture 1-like gene.Transcriptome data analysis showed that Car-miR156a/c/d/f were expressed in 8 tissues of chickpea,Car-miR156b was not expressed in root,and Car-miR156e was not expressed in stem and flower.These findings provide the basis for studying the expression of the Car-miR156 family members and the function of their target genes.