巨桉miRNA及其靶基因生物信息学预测

Bioinformatic analysis of microRNA and their target genes in Eucalyptus grandis

[目的]识别并筛选与巨桉木质形成相关的miRNA基因,为开展巨桉遗传品质改良奠定基础.[方法]将mirBase数据库中所有植物的3228条miRNA序列提交到psRobot网站进行茎环结构预测,然后应用BLAST-2.2.27＋软件与rfam和pfam数据库比对后去除非miRNA序列,应用Bioedit分析miRNA序列及前体序列的碱基组成特点.[结果]共预测获得341条miRNA前体序列和129条成熟的miRNA序列,属于28个不同miRNA家族.预测的巨桉miRNA长度为18～23 bp.其中长度为21个碱基的miRNA数量最多,达76个,miRNA前体长度为71～221 bp,平均长度为123 bp.巨桉miRNA序列和其侧翼序列均存在碱基偏倚现象,5＇端第1碱基尿嘧啶出现的频率高达62.8％,第19碱基以胞嘧啶出现的频率最高,miRNA下游侧翼序列第1碱基G出现的频率仅为9.1％.靶基因预测发现,与木质形成相关的miRNA有41个,其中34个调节与木质形成相关的转录因子,主要调控ARF、HD-ZIPIII、KAN、MYB和NAC;10个调节与木质形成相关的酶,主要调控肉桂酰CoA还原酶、肉桂醇脱氢酶、纤维素合成酶、过氧化物酶和漆酶.[结论]巨桉中存在41个与木质形成相关的miRNA基因,可应用于巨桉遗传品质的改良研究.

[Objective ]The present study was conducted to identify and select miRNA genes related to xylon for- mation of Eucalyptus grandis in order to lay a theoretical foundation on genetic quality improvement of Eucalyptus grandis variety. [Method]Prediction of stem-loop structure of pre-miRNAs was run on the web-based software psRobot using 3228 miRNA sequences of all plants from mirBase database. Non-miRNA sequences were removed by BLAST search against rfam and pfam database. The characteristics of base composition in miRNA sequences and their precursors were analyzed by Bioedit software. [Result ]Among 3228 miRNA sequences, 341 miRNA precursor se- quences and 129 mature miRNAs were found, which belong to 28 different miRNA familes. The predicted miRNA length of Eucalyptus grandis ranged from 18 to 23 bp, and the miRNAs of 21 bp in length was at most（76）. The miRNA precursor ranged from 71 to 221 bp, and the average was 123 bp. Nucleotide bias of miRNA was found not only in miRNA mature sequences, but also in flanking sequences. Comparative sequence analysis of mature miRNA sequences, it showed that uracil was the dominant at the 1~ base of the 5＇-end, which was up to 62.8%, while cy- tosine is dominant at the 194 base. At the same time, the frequency of G was only 9.1% at the 1^st base in miRNA downstream flanking sequences. Target gene prediction results showed that 41 miRNAs were considered as regulate gene for xylon formation. Out of which, 34 miRNAs may be the transcription factors, viz., ARF, HD-ZIPIII, KAN, MYB and NAC; while 10 miRNAs were involved in enzyme of xylon formation, which mainly regulate cinnamyl alco- hol dehydrogenase, peroxidase and cellulose synthase, etc. [Conclusion]There are 41 miRNAs related to xylon formation of Eucalyptus grandis, which would be applied on improvement of genetic quality.