Identification and characterization of long non-coding RNAs involved in the formation and development of poplar adventitious roots
Identification and characterization of long non-coding RNAs involved in the formation and development of poplar adventitious roots
复制标题
杨树不定根形成和发育中涉及的长非编码RNA的鉴定和表征
DOI：
10.1016/j.indcrop.2018.03.071
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发表时间：
2018-08-01
影响因子：
5.9
通讯作者：
Xu, Meng
中科院分区：
文献类型：
--
作者：
Liu, Sian;Sun, Zimou;Xu, Meng
不定根是经济上重要的木本植物无性繁殖所必需的。更好地了解促进或阻碍生根的遗传和生理机制将提高树木成功商业部署的潜力。越来越多的证据表明，长链非编码rna （lncRNAs）在广泛的生物过程中起着至关重要的调节作用。近年来，随着高通量测序技术的快速发展，在植物中已经发现了大量的incrna，但木本植物中的incrna在很大程度上仍然未知。本研究在全基因组范围内系统鉴定和表征了杨树不定根不同发育阶段表达的lncrna。通过计算分析，我们确定了5952种可能的lncrna: 4481种基因间lncrna， 761种反义lncrna和710种内含子lncrna，并分析了它们的结构和表达水平差异。我们还分析了蛋白编码基因和lncrna之间的表达水平差异。这34个差异表达基因被144个lncrna顺式调控，为生长素调控不定根发育提供了新的视角。此外，还鉴定了参与杨树根系发育的IncWOX5和incWOX11的lncrna，并对其进行了表征：lncWOX5负调控WOX5， lncWOX11正调控WOX11。我们对IncWOX5和lnwox11的发现和表征，使我们对不定根的形成和发育有了更清晰的认识，并初步建立了不定根形成和发育的理论框架。
Adventitious rooting is essential for vegetative propagation of economically important woody species. A better understanding of the genetic and physiological mechanisms that promote or hinder rooting will enhance the potential for successful commercial deployment of trees. Increasing evidence shows that long non-coding RNAs (lncRNAs) play crucial regulatory roles in a wide range of biological processes. Although a large number of IncRNAs have been identified in plants due to the rapid development of high-throughput sequencing technology in recent years, those in woody plants remain largely unknown. Here, we systematically identified and characterized lncRNAs expressed in different developmental stages of poplar adventitious roots at a genome-wide scale. Through computational analysis, we identified 5952 putative lncRNAs: 4481 intergenic lncRNAs, 761 anti sense lncRNAs and 710 intronic lncRNAs-for which the structure and expression level differences were analyzed. We also analyzed the different expression levels between protein-coding genes and lncRNAs. The 34 differentially expressed genes were regulated by 144 lncRNAs in cis-action, which provided a new perspective for the regulation of auxin in adventitious root development. In addition, lncRNAs of both IncWOX5 and incWOX11, which are involved in poplar root development were identified and characterized: lncWOX5 negatively regulated WOX5 and lncWOX11 positively regulated WOX11. Our discovery and characterization of IncWOX5 and lncWOX11 allow for a clearer understanding and preliminarily establishing a theoretical framework for adventitious root formation and development.