Xu Qin, Song Zhihong, Zhu Caiyun, Tao Chengcheng, Kang Lifang, Liu Wei, He Fei, Yan Juan, Sang Tao
Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Plant Biol. 2017 Feb 13;17(1):42. doi: 10.1186/s12870-017-0984-8.
Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change are still poorly understood. Here we identified 17,610 lncRNAs and calculated their expression levels based on RNA-seq of 80 individuals of Miscanthus lutarioriparius from two environments, the nearly native habitats and transplanted field, respectively.
LncRNAs had significantly higher expression diversity and lower expression frequency in population than protein coding mRNAs in both environments, which suggested that lncRNAs may experience more relaxed selection or divergent evolution in population compared with protein coding RNAs. In addition, the increase of expression diversity for lncRNAs was always significantly higher and the magnitude of fold change of expression in new stress environment was significantly larger than protein-coding mRNAs. These results suggested that lncRNAs may be more sensitive to environmental change than protein-coding mRNAs. Analysis of environment-robust and environment-specific lncRNA-mRNA co-expression network between two environments revealed the characterization of lncRNAs in response to environmental change. Furthermore, candidate lncRNAs contributing to water use efficiency (WUE) identified based on the WUE-lncRNA-mRNA co-expression network suggested the roles of lncRNAs in response to environmental change.
Our study provided a comprehensive understanding of expression characterization of lncRNAs in population for M. lutarioriparius under field condition, which would be useful to explore the roles of lncRNAs and could accelerate the process of adaptation in new environment for many plants.
长链非编码RNA（lncRNA）是一类在生物体生物学过程中具有重要调控作用的非编码RNA。lncRNAs与蛋白质编码mRNA在群体表达及其对环境变化的反应方面的系统比较仍知之甚少。在此，我们分别基于来自两个环境（近乎原生栖息地和移植田地）的80个卢氏芒个体的RNA测序，鉴定了17,610个lncRNAs并计算了它们的表达水平。
在两种环境中，lncRNAs在群体中的表达多样性显著高于蛋白质编码mRNA，而表达频率则低于蛋白质编码mRNA，这表明与蛋白质编码RNA相比，lncRNAs在群体中可能经历了更宽松的选择或分歧进化。此外，lncRNAs表达多样性的增加总是显著高于蛋白质编码mRNA，并且在新的胁迫环境中表达变化倍数的幅度也显著更大。这些结果表明，lncRNAs可能比蛋白质编码mRNA对环境变化更敏感。对两个环境之间环境稳健和环境特异性lncRNA-mRNA共表达网络的分析揭示了lncRNAs对环境变化的响应特征。此外，基于水分利用效率（WUE）-lncRNA-mRNA共表达网络鉴定的有助于水分利用效率的候选lncRNAs表明了lncRNAs在响应环境变化中的作用。
我们的研究全面了解了田间条件下卢氏芒群体中lncRNAs的表达特征，这将有助于探索lncRNAs的作用，并可加速许多植物在新环境中的适应过程。
