Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes.
Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes.
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DOI：
10.1016/j.gene.2018.07.043
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发表时间：
2018-11
期刊：
影响因子：
3.5
通讯作者：
Z. Qiu;Yanyan He;Yimeng Zhang;Junli Guo;Liang Zhang
中科院分区：
文献类型：
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作者：
Z. Qiu;Yanyan He;Yimeng Zhang;Junli Guo;Liang Zhang
microRNA（miRNAs）是一类内源性非编码小RNA，在转录后水平对基因表达起重要调控作用。毛泡桐生长迅速，是一种重要的生态经济树种，但对冬夏过渡期形成层组织中的小分子RNA（small RNAs，sRNAs）的研究较少。在本研究中，我们鉴定了33个已知的miRNA家族和29个新的miRNA，其中包括20个推定的新的miRNA * inP。冬夏过渡期的被毛囊形成层组织。通过差异表达分析，我们发现15个已知的miRNAs和8个新的miRNAs在形成层组织的某个阶段优先富集。基于P. tomentosamRNA转录组数据库中，对29种已知和20种新的miRNAs分别预测了1667个和78个潜在靶点，预测的靶点主要是转录因子和功能基因。利用Gene Ontology富集分析技术对这些miRNAs的靶点进行了“代谢过程”和“转录调控”的富集。此外，KEGG途径分析揭示了miRNA参与淀粉和蔗糖代谢以及植物-病原体相互作用代谢途径。qRT-PCR结果显示，9种miRNAs与其靶基因表达呈负相关。被毛囊形成层组织这项研究是第一个研究已知和新的miRNAs及其潜在的靶点。通过对冬夏过渡期树木形成层发育过程中的微RNA表达的研究，筛选出了几个可能调控形成层发育过程的候选基因，为进一步研究miRNAs在树木形成层发育过程中的调控和木材形成过程中的作用提供了理论基础。
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, have been shown to play essential roles in the regulation of gene expression at the post-transcriptional level. AlthoughPaulownia tomentosais an ecologically and economically important timber species due to its rapid growth, few efforts have focused on small RNAs (sRNAs) in the cambial tissues during winter and summer transition. In the present study, we identified 33 known miRNA families and 29 novel miRNAs which include 20 putative novel miRNAs* inP. tomentosacambial tissues during winter and summer transition. Through differential expression analysis, we showed that 15 known miRNAs and 8 novel miRNAs were preferentially abundant in certain stage of cambial tissues. Based on theP. tomentosamRNA transcriptome database, 1667 and 78 potential targets were predicted for 29 known and 20 novel miRNAs, respectively and the predicted targets are mostly transcription factors and functional genes. The targets of these miRNAs were enriched in “metabolic process” and “transcription regulation” by using Gene Ontology enrichment analysis. In addition, KEGG pathway analyses revealed the involvement of miRNAs in starch and sucrose metabolism and plant-pathogen interaction metabolism pathways. Noticeably, qRT-PCR expression analysis demonstrated that 9 miRNAs and their targets were existed a negative correlation inP. tomentosacambial tissues. This study is the first to examine known and novel miRNAs and their potential targets inP. tomentosacambial tissues during winter and summer transition and identify several candidate genes potentially regulating cambial phase transition, and thus provide a framework for further understanding of miRNAs functions in the regulation of cambial phase transition and wood formation in trees.