基于全基因组预测莱茵衣藻的新miRNA及其靶基因

Genome-wide analysis of miRNAs and target prediction in Chlamydomonas reinhardtii

莱茵衣藻(Chlamydomonas reinhardtii)是一种重要的模式生物,其miRNA的发现相对较晚.为系统化地预测分析莱茵衣藻的miRNA,采用比较基因组和同源比对相结合的方法,根据mi Rbase中已知的莱茵衣藻miRNA序列以及前体的特点,并且基于莱茵衣藻的全基因组对其miRNA的前体序列和成熟miRNA进行系统的分析和筛选,使用unigene和JGI的莱茵衣藻相关序列数据库对预测结果进行靶基因预测和功能的分析.最终发现可能存在的miRNA 36条,其前体结构符合miRNA前体的基本特征且具有高度的同源性,两个数据库所得相匹配靶基因分别为64和32条,其中部分是与莱茵衣藻各项生命活动相关的基因.本研究表明莱茵衣藻的基因组中具有可能存在的新miRNA家族,并且部分有高度匹配的靶基因,为其后续研究提供了可靠的理论支持.

Chlamydomonas reinhardtii is an important model organism,but its miRNA is not fully understood.Therefore,systemic prediction and analysis of Chlamydomonas reinhardtii miRNA is of important significance for further researches.This study aimed to set up the parameters including GC content of pre-miRNA,number of loops in pre-miRNA secondary structure,size of loop,folding free energy and minimal folding free energy index,using the genome and homologous alignment method in combination with the characteristics of known 85 miRNA sequences and precursors of Chlamydomonas reinhardtii in miRbase.Based on the whole genome,the miRNA precursor sequences and mature miRNA were systemically analyzed and screened.Finally the softwares psRNATarget and psRobot were used based on the sequence data of Chlamydomonas reinhardtii from the unigene and JGI genomic databases to Conduct target gene prediction and functional analysis of prediction results.All together 36 possible miRNAs were defined,with the two softwares obtaining 64 and 32 matched target genes respectively.The result indicated probable existence of a new miRNA family with some highly matched target genes in Chlamydomonas reinhardtii genome.