title: Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens.
abstract: BACKGROUND
  The functional repertoire of long noncoding RNA (lncRNA) has been characterized in several model organisms, demonstrating that lncRNA plays important roles in fundamental biological processes. However, they remain largely unidentified in most species. Understanding the characteristics and functions of lncRNA in insects would be useful for insect resources utilization and sustainable pest control.
  
  
  METHODS
  A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper, Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.
  
  
  RESULTS
  In total, 2,439 lncRNA transcripts corresponding to 1,882 loci were detected from 12 whole transcriptomes (RNA-seq) datasets, including samples from high fecundity (HFP), low fecundity (LFP), I87i and C89i populations, in addition Mudgo and TN1 virulence strains. The identified N. lugens lncRNAs had low sequence similarities with other known lncRNAs. However, their structural features were similar with mammalian counterparts. N. lugens lncRNAs had shorter transcripts than protein-coding genes due to the lower exon number though their exons and introns were longer. Only 19.9% of N. lugens lncRNAs had multiple alternatively spliced isoforms. We observed biases in the genome location of N. lugens lncRNAs. More than 30% of the lncRNAs overlapped with known protein-coding genes. These lncRNAs tend to be co-expressed with their neighboring genes (Pearson correlation, p < 0.01, T-test) and might interact with adjacent protein-coding genes. In total, 19-148 lncRNAs were specifically-expressed in the samples of HFP, LFP, Mudgo, TN1, I87i and C89i populations. Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.
  
  
  CONCLUSIONS
  The structural features of N. lugens lncRNAs are similar to mammalian counterparts. Coexpression and function analysis suggeste that N. lugens lncRNAs might have important functions in high fecundity and virulence adaptability.
  
  
  CONCLUSIONS
  This study provided the first catalog of lncRNA genes in rice brown planthopper. Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.|Department of City Construction, Shaoyang University, Shaoyang, 422000, China.
authors.forename: Huamei
authors.initials: H
authors.lastname: Xiao
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Zhuting
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Dianhao
authors.initials: D
authors.lastname: Guo
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Bofeng
authors.initials: B
authors.lastname: Hou
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Chuanlin
authors.initials: C
authors.lastname: Yin
authors.affiliation: State Key Laboratory for Biocontrol/Institute of Entomology, Sun Yat Sen University, Guangzhou, 510275, China.
authors.forename: Wenqing
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China. lifei18@zju.edu.cn.|Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China. lifei18@zju.edu.cn.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D016000:Cluster Analysis; D005298:Fertility / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023061:Gene Order; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D006430:Hemiptera / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000469:parasitology*; D010935:Plant Diseases / Q000469:parasitology; D062085:RNA, Long Noncoding; D015203:Reproducibility of Results; D014774:Virulence / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding