title: Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change.
abstract: 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.
authors.affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Xu
authors.affiliation: 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.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Song
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.|University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Caiyun
authors.initials: C
authors.lastname: Zhu
authors.affiliation: 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.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Tao
authors.affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Kang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: He
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Yan
authors.affiliation: Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. sang@ibcas.ac.cn.|State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China. sang@ibcas.ac.cn.
authors.forename: Tao
authors.identifier: 0000-0001-6526-5147
authors.initials: T
authors.lastname: Sang
mesh_terms: D002681:China; D017753:Ecosystem; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D006109:Poaceae / Q000235:genetics* / Q000502:physiology; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant; D014867:Water / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D018749:RNA, Plant; D014867:Water
keywords: Co-expression; Environmental response; Expression diversity; Miscanthus lutarioriparius; Population transcriptome; lncRNAs