title: Transcriptome and gene expression analysis of the rice leaf folder, Cnaphalocrosis medinalis.
abstract: BACKGROUND
  The rice leaf folder (RLF), Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Pyralidae), is one of the most destructive pests affecting rice in Asia. Although several studies have been performed on the ecological and physiological aspects of this species, the molecular mechanisms underlying its developmental regulation, behavior, and insecticide resistance remain largely unknown. Presently, there is a lack of genomic information for RLF; therefore, studies aimed at profiling the RLF transcriptome expression would provide a better understanding of its biological function at the molecular level.
  
  
  RESULTS
  De novo assembly of the RLF transcriptome was performed via the short read sequencing technology (Illumina). In a single run, we produced more than 23 million sequencing reads that were assembled into 44,941 unigenes (mean size = 474 bp) by Trinity. Through a similarity search, 25,281 (56.82%) unigenes matched known proteins in the NCBI Nr protein database. The transcriptome sequences were annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). Additionally, we profiled gene expression during RLF development using a tag-based digital gene expression (DGE) system. Five DGE libraries were constructed, and variations in gene expression were compared between collected samples: eggs vs. 3(rd) instar larvae, 3(rd) instar larvae vs. pupae, pupae vs. adults. The results demonstrated that thousands of genes were significantly differentially expressed during various developmental stages. A number of the differentially expressed genes were confirmed by quantitative real-time PCR (qRT-PCR).
  
  
  CONCLUSIONS
  The RLF transcriptome and DGE data provide a comprehensive and global gene expression profile that would further promote our understanding of the molecular mechanisms underlying various biological characteristics, including development, elevated fecundity, flight, sex differentiation, olfactory behavior, and insecticide resistance in RLF. Therefore, these findings could help elucidate the intrinsic factors involved in the RLF-mediated destruction of rice and offer sustainable insect pest management.
authors.affiliation: Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, China.
authors.forename: Shang-Wei
authors.initials: SW
authors.lastname: Li
authors.forename: Hong
authors.initials: H
authors.lastname: Yang
authors.forename: Yue-Feng
authors.initials: YF
authors.lastname: Liu
authors.forename: Qi-Rong
authors.initials: QR
authors.lastname: Liao
authors.forename: Juan
authors.initials: J
authors.lastname: Du
authors.forename: Dao-Chao
authors.initials: DC
authors.lastname: Jin
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005260:Female; D005426:Flight, Animal; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D017344:Genes, Insect / Q000235:genetics; D008658:Inactivation, Metabolic / Q000235:genetics; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism; D007306:Insecticides / Q000633:toxicity; D007915:Lepidoptera / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D008297:Male; D058977:Molecular Sequence Annotation; D009132:Muscles / Q000378:metabolism; D012275:Oryza / Q000469:parasitology*; D010802:Phylogeny; D018515:Plant Leaves / Q000469:parasitology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018035:Receptors, Odorant / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012727:Sex Characteristics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D019476:Insect Proteins; D007306:Insecticides; D012333:RNA, Messenger; D018035:Receptors, Odorant; C045648:odorant-binding protein