Table_6_Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S.XLSX

Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.

长链非编码RNA（long non-coding RNAs，lncRNAs）作为多种生物学过程的通用调控因子，但目前尚无针对参与光温敏核雄性不育（photo-thermosensitive genic male sterile，PTGMS）水稻品系育性转换的长链非编码RNA开展全基因组筛选的相关报道。本研究对新型光温敏核雄性不育水稻品系武香S（Wuxiang S，WXS）的三个发育阶段进行了链特异性RNA测序，共鉴定出3948个长链非编码RNA；其中622个为雄性不育武香S（WXS-S）与雄性可育武香S（WXS-F）之间的差异表达长链非编码RNA（differentially expressed lncRNAs，DE-lncRNAs）。大量差异表达长链非编码RNA在花粉母细胞减数分裂阶段呈现表达差异，提示该阶段可能是武香S育性转换的关键时期。此外，对差异表达长链非编码RNA的顺式和反式靶标进行功能注释后发现，对应141个差异表达长链非编码RNA的150个靶标参与了花药与花粉发育过程。进一步的计算分析预测，97个长链非编码RNA可作为72个microRNA（miRNA）的前体，同时94个差异表达长链非编码RNA可作为150个microRNA的潜在内源靶标模拟物（endogenous target mimics，eTMs）。最后，通过双荧光素酶报告基因实验（dual luciferase reporter assays）验证发现，2个长链非编码RNA分别通过竞争性结合共享的osa-miR156和osa-miR396，作为内源靶标模拟物调控SPL基因与GRF基因的表达。本研究揭示的长链非编码RNA的基因组特征、表达差异及其与microRNA（miRNA）和信使RNA（messenger RNA，mRNA）的相互作用，有助于深化对长链非编码RNA在光温敏核雄性不育水稻品系育性转换过程中调控作用的理解。