Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China.
Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Int J Mol Sci. 2021 Apr 29;22(9):4742. doi: 10.3390/ijms22094742.
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice ssp. and ssp. , and their wild progenitor . We identified a total of 8528 lncRNAs, including 4072 lncRNAs in , 2091 lncRNAs in rice, and 2365 lncRNAs in rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
作物驯化产生了许多理想的农艺性状，是植物进化的典型模式系统。大量的基因组证据表明，非编码 RNA（如 microRNAs 和 phasiRNAs）以及蛋白编码基因在作物驯化过程中受到选择。然而，有限的数据表明植物长非编码 RNA（lncRNAs）也参与了这一生物学过程。在这项研究中，我们对栽培稻亚种 和 及其野生祖本 进行了链特异性 RNA 测序。我们总共鉴定了 8528 个 lncRNAs，其中 中有 4072 个， 中有 2091 个， 中有 2365 个。与栽培稻中的 lncRNAs 相比，野生稻中表达的 lncRNAs 长度更短，外显子数量更少。我们还鉴定了野生和栽培稻中一些保守的 lncRNAs。功能研究表明，这些保守的 lncRNAs 中的几个与水稻驯化相关的性状有关。我们的研究结果揭示了 lncRNAs 在水稻驯化过程中的特征和保守性，并将进一步促进水稻 lncRNAs 的功能研究。
