Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in .

Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two species ( and ) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of lncRNAs showed limited sequence conservation among 39 species, which implied that -specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the -regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between and , 128 lncRNA-PCG pairs were obtained in , whereas 92 lncRNA-PCG pairs were obtained in . In addition, a total of 19 lncRNA-PCG pairs in and 14 lncRNA-PCG pairs in were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between and were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in , laying the groundwork for further exploration into the biological function of in environmental adaptation.