LncRNA在稻属AA-基因组8个物种中序列与功能的进化研究

LncRNA plays important roles in a wide range of biological processes, including chromatin state formation and gene expression regulation, but its origin, evolution and interaction with genome are unclear. Our recent study showed that 2014 Oryza sativa lncRNAs were also detected in 7 other AA-genome Oryza species, and 30% of lncRNAs were conserved among 8 species. In addition, as the speciation evolved, lncRNA expression diversified more greatly between species than tissues, suggesting that Oryza AA genome was a suitable model for the study of lncRNA evolution. In order to reveal the evolution patterns of sequence, structure, expression and function of lncRNA among AA-genome Oryza species, we are to conduct rebio-zero strand RNA-sequencing, systematic and genome-wide analysis and group sample experimental test. This will be conducive to elucidating the roles of lncRNA in Oryza speciation and genome evolution, and providing a database for application of functionally important lncRNA in rice breeding practice.

LncRNA在基因组结构形成和基因表达调控等过程中起着重要的作用，但其起源、进化及其与基因组的互作尚不清楚。在前期研究中，我们发现水稻中2014条lncRNA在其它7个稻属AA基因组物种中也有表达，其中30%的lincRNA在8物种中序列保守性较高，并随着物种分化时间增加其表达量的种间差异逐渐超过组织差异，表明这组快速分化的物种非常适合作为植物中lncRNA进化研究模型。本项目计划通过链特异转录本测序、比较基因组学分析与群体样本实验验证，对8个稻属AA基因组物种中的lncRNA进行系统分析，鉴定物种特异lncRNA，评估lncRNA进化速率与剪接模式的变化规律，分析表达动态与系统功能的进化模式。本项目的实施有助于阐明lncRNA在稻属物种分化及基因组进化中的作用，并为在水稻育种实践中合理利用重要功能lncRNA提供数据基础。

基于该项目的支持，我们对稻属AA基因组9个物种的4个组织进行全转录组测序与lncRNA的分析，获得了48203条长链非编码RNA（lncRNA）。我们找到了2808条物种特异的lncRNA，341条保守lncRNA，266条lncRNA可能是miRNA的前体，397条lncRNA可能是snoRNA的前体。LncRNA在染色体上的分布具有一定规律，与mRNA相比，lncRNA的保守性较差，在进化过程中基因组上一些位点尽管还保留有相似序列但是已失去表达能力。DNA转座子在稻属lncRNA外显子序列的快速进化起到重要作用，而LTR逆转录转座子更多影响了lncRNA的内含子及可变剪接。稻属AA基因组物种间lncRNA的表达差异远大于mRNA，并且在亚洲栽培稻及其祖先种的分析中显示出营养器官和繁殖器官之间的变化差异。筛选出来的重要差异lncRNA为水稻育种中挖掘抗逆和高非生物适应性位点提供了大量新的数据支持。