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

Simple Summary: Orinus, a genus distributed in alpine regions of the Qinghai-Xizang (Tibet) Plateau (QTP), includes the following two species: O. thoroldii, predominantly in the western QTP at elevations between 3300 and 4700 m, and O. kokonoricus, in the eastern QTP at relatively low altitude between 2500 and 3400 m. However, the mechanism of long noncoding RNA (lncRNA)-regulated speciation adaptation to high altitudes and cold arid environments in Orinus remains unclear. In this study, we first identified the transcriptome-wide features of lncRNAs in O. thoroldii and O. kokonoricus, including five main types of lncRNAs that class_code with "i, o, u, x, j". Then, an evolutionary tree was conducted to implicate the relationships among 39 species with the count of conserved lncRNAs. Moreover, we sought to reveal the mechanism of cis-regulation from differentially expressed lncRNAs (DElncRNAs) and their nearby protein-coding genes (PCGs) between O. thoroldii and O. kokonoricus. GO analysis showed that DElncRNAs and their potential target PCGs participate in different biological processes between O. thoroldii and O. kokonoricus, indicating their speciation adaptation on the QTP. In addition, the specifically expressed transcription factors (TFs) in O. thoroldii suggested that DElncRNAs play a vital role in adapting to the environment through the expressed regulation of TFs. 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 Orinus 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 Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus 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 O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation. [ABSTRACT FROM AUTHOR]