Abstract
BackgroundLong 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.ResultsLncRNAs 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.ConclusionOur 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.
Highlights
Long non-coding RNA is a class of non-coding RNA with important regulatory roles in biological process of organisms
Relaxed expression regulation of Long non-coding RNA (lncRNA) and more sensitive to environment compared with protein coding mRNAs In our study, we found the expression diversity of lncRNAs were significantly higher than that of protein coding RNAs in both Jiangxia of Hubei Province (JH) and Qingyang of Gansu Province (QG), the two independent strictly controlled experiments (Fig. 3a)
In this study, we identified population-wide lncRNAs in M. lutarioriparius under two different field conditions
Summary
Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. LncRNAs have lower level of sequence conservation than protein-coding mRNAs [2] They were originally considered as transcriptional by-products or “expression noise” of protein coding genes and were often dismissed in analyses of transcriptome [3], recent studies uncovered the increasing body of evidences that lncRNAs strictly regulated and played important roles in biological process of organisms [4]. A great number of lncRNAs had been identified in animals and humans [5,6,7,8,9,10,11] They participated in numerous biological processes, such as X-chromosome inactivation [12], and human diseases [6,7,8, 13, 14], only a few of them have been functionally annotated. Most of the annotated lncRNAs are related with regulation of the development of plants
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