title: Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.
abstract: Long intergenic noncoding RNAs (lincRNAs) are intergenic transcripts with a length of at least 200 nt that lack coding potential. Emerging evidence suggests that lincRNAs from animals participate in many fundamental biological processes. However, the systemic identification of lincRNAs has been undertaken in only a few plants. We chose to use cucumber (Cucumis sativus) as a model to analyze lincRNAs due to its importance as a model plant for studying sex differentiation and fruit development and the rich genomic and transcriptome data available. The application of a bioinformatics pipeline to multiple types of gene expression data resulted in the identification and characterization of 3,274 lincRNAs. Next, 10 lincRNAs targeted by 17 miRNAs were also explored. Based on co-expression analysis between lincRNAs and mRNAs, 94 lincRNAs were annotated, which may be involved in response to stimuli, multi-organism processes, reproduction, reproductive processes, and growth. Finally, examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, while 16 lincRNAs are under natural selection. Our results provide a rich resource for further validation of cucumber lincRNAs and their function. The identification of lincRNAs targeted by miRNAs offers new clues for investigations into the role of lincRNAs in regulating gene expression. Finally, evaluation of the lincRNAs suggested that some lincRNAs are under positive and balancing selection.
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China; Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Zhiqiang
authors: Z
authors: Hao
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Chunyan
authors: C
authors: Fan
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Tian
authors: T
authors: Cheng
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Ya
authors: Y
authors: Su
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Qiang
authors: Q
authors: Wei
authors: College of Life Sciences, Shaanxi Normal University, Xi'an, China; Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an, China.
authors: Guanglin
authors: G
authors: Li
mesh_terms: D017124:Conserved Sequence; D018553:Cucumis sativus / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D023281:Genomics; D009928:Organ Specificity; D011110:Polymorphism, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D018749:RNA, Plant