Oryza sativa Indica Group cultivar:DX142 Transcriptome or Gene expression. Oryza sativa Indica Group cultivar:DX142

Long non-coding RNAs (lncRNAs) have been realized to play an important role in several gene regulatory networks involved in various biological processes of plants stress response. However, systematic analysis of lncRNAs expressed in rice Cadmium (Cd) stress are limited. Thus, we presented the expression and characterization of lncRNAs in rice roots development at early stage in response to Cd stress.The lncRNA deep sequencing revealed differentially expressed lncRNAs between Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up regulated and 75 were down regulated. Otherwise, 386 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis were detected, and target gene-related pathway analysis showed significant changes in cysteine and methionine metabolism pathway related genes. For the trans, a total of 28,276 interaction relationships were detected between 144 lncRNAs and the differentially expressed protein-coding genes. The pathway analyses found that secondary metabolites such as phenylpropanoids and phenylalanine and photosynthesis pathways related genes were significantly altered by Cd stress. All these results indicate that lncRNAs may regulate genes of cysteine-rich peptides metabolism in cis and the secondary metabolites and photosynthesis in trans, then activated various physiological and biochemical reactions to response to excessive Cd. The present study provides a valuable resource for lncRNA studies in response to Cd treatment in rice. It expands our knowledge about lncRNA biology function as well as contributes to the annotation of the rice genome.

长链非编码RNA（Long non-coding RNAs，以下简称lncRNAs）现已被证实可参与调控植物胁迫响应相关多种生物学过程的基因调控网络，并发挥关键作用。然而，针对水稻镉（Cadmium，Cd）胁迫下表达的lncRNAs的系统性分析仍较为匮乏。为此，本研究对水稻早期根系响应镉胁迫过程中的lncRNAs表达谱与特征进行了系统解析。通过lncRNA深度测序，本研究鉴定得到了镉胁迫与正常培养条件下的差异表达lncRNAs。在镉胁迫组中，共有69个lncRNAs呈上调表达，75个呈下调表达。此外，本研究共检测到120个差异表达lncRNAs与362个顺式（cis）作用差异表达基因之间形成的386个lncRNA-mRNA配对；靶基因通路富集分析显示，半胱氨酸与甲硫氨酸代谢通路相关基因的表达发生了显著变化。针对反式（trans）作用，本研究共检测到144个lncRNAs与差异表达蛋白编码基因之间形成的28276条互作关系。通路富集分析结果表明，苯丙烷类、苯丙氨酸等次生代谢产物及光合作用通路相关基因的表达均受镉胁迫影响而发生显著改变。上述结果显示，lncRNAs可通过顺式作用调控富半胱氨酸肽类代谢相关基因，并通过反式作用调控次生代谢与光合作用相关基因，进而激活一系列生理生化反应以应对过量镉胁迫。本研究为水稻响应镉胁迫的lncRNAs研究提供了宝贵的数据集资源，不仅拓展了我们对lncRNA生物学功能的认知，也为水稻基因组注释工作提供了重要参考。