Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis

Abstract

BackgroundThe 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.Principal Findings 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. 3rd instar larvae, 3rd 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).ConclusionsThe 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.

First Transcriptome and Digital Gene Expression Analysis in Neuroptera with an Emphasis on Chemoreception Genes in Chrysopa pallens (Rambur)

“…To better understand the sophisticated olfactory system of C. pallens , 66 putative chemoreception genes(including OBPs , CSPs , ORs , IRs , and SNMPs ) were identified from our transcriptome. This number is more than the numbers found in Cnaphalocrosis medinalis (22) [41] and Cotesia vestalis (28) [42], but less than that of Spodoptera littoralis (82) [30], Manduca sexta (94) [43] and Helicoverpa armigera (99) [34].…”

Differential Expression Patterns in Chemosensory and Non-Chemosensory Tissues of Putative Chemosensory Genes Identified by Transcriptome Analysis of Insect Pest the Purple Stem Borer Sesamia inferens (Walker)

“…After clustering and redundancy filtering, we finally acquired 56,210 unigenes (≥150 bp) with a mean length of 394 bp and the N50 length of 460 bp. We called these 56,210 ones unigenses according to some recently published papers [33], [46], although each of them may not necessarily represents a unique gene. Of the 56,210 unigenes, those with a sequence length more than 500 bp accounted for 20.41% of the transcriptome assembly (Figure 1).…”

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

“…Although the sequencing of large genomes remains expensive, even using NGS technologies [4], transcriptome sequencing can provide information regarding the gene content of a species and can complement genome sequencing approaches.…”