The developmental transcriptome of the bamboo snout beetle Cyrtotrachelus buqueti and insights into candidate pheromone-binding proteins

Abstract

Cyrtotrachelus buqueti is an extremely harmful bamboo borer, and the larvae of this pest attack clumping bamboo shoots. Pheromone-binding proteins (PBPs) play an important role in identifying insect sex pheromones, but the C. buqueti genome is not readily available for PBP analysis. Developmental transcriptomes of eggs, larvae from the first instar to the prepupal stage, pupae, and adults (females and males) from emergence to mating were built by RNA sequencing (RNA-Seq) in the present study to establish a sequence background of C. buqueti to help understand PBPs. Approximately 164.8 million clean reads were obtained and annotated into 108,854 transcripts. These were assembled into 24,338, 21,597, 24,798, 21,886, 24,642, and 83,115 unigenes for eggs, larvae, pupae, females, males, and the combined datasets, respectively. Unigenes were annotated against NCBI non-redundant protein sequences, NCBI non-redundant nucleotide sequences, Gene Ontology (GO), Protein family, Clusters of Orthologous Groups of Proteins/ Clusters of Eukaryotic Orthologous Groups (KOG), Swiss-Prot, and KEGG Orthology databases. A total of 17,213 unigenes were annotated into 55 sub-categories belonging to three main GO categories; 10,672 unigenes were classified into 26 functional categories by KOG classification, and 8,063 unigenes were classified into five functional KEGG categories. RSEM software for RNA sequencing showed that 4,816, 3,176, 3,661, 2,898, 4,316, 8,019, 7,273, 5,922, 5,844, and 4,570 genes were differentially expressed between larvae and males, larvae and eggs, larvae and pupae, larvae and females, males and females, males and eggs, males and pupae, females and eggs, females and pupae, and eggs and pupae, respectively. Of these, three were confirmed to be significantly differentially expressed between larvae, females, and males. Furthermore, PBP Cbuq7577_g1 was highly expressed in the antenna of males. A comprehensive sequence resource of a desirable quality was constructed from developmental transcriptomes of C. buqueti eggs, larvae, pupae, and adults. This work enriches the genomic data of C. buqueti, and facilitates our understanding of its metamorphosis, development, and response to environmental change. The identified candidate PBP Cbuq7577_g1 might play a crucial role in identifying sex pheromones, and could be used as a targeted gene to control C. buqueti numbers by disrupting sex pheromone communication.

Transcriptome analysis in different developmental stages of Batocera horsfieldi (Coleoptera: Cerambycidae) and comparison of candidate olfactory genes

“…Specific primer pairs were derived from the transcriptome data, and primer pairs for each gene were designed to amplify 100–200 bp products, which were verified by sequencing. A semi-quantitative RT-PCR (Bio-Rad S1000, US) analysis was performed for each primer pair using r Taq DNA polymerase (Takara, Dalian, Liaoning, China) before the RT-qPCR analysis to ensure that the correct products were amplified and no primer dimers were present [ 53 ]. The RT-qPCR analysis was carried out using an Mx 3000P detection system (Agilent, Palo Alto, CA, USA) as described previously, with thermal cycler parameters of 2 min at 94°C, then 40 cycles of 20 s at 94°C, 20 s at 58°C, and 20 s at 72°C.…”

De novo transcriptome assembly of the bamboo snout beetle Cyrtotrachelus buqueti reveals ability to degrade lignocellulose of bamboo feedstock

“…The de novo developmental transcriptome of C. buqueti comprised 31,469,916, 36,773,825, 32,128,345, 33,070,448 and 31,434,121 clean reads in eggs, larvae, pupae, female and male imagos, respectively, with a total of 108,854 transcripts obtained and assembled into 83,115 unigenes [ 35 ].…”

“…Transcriptomes from five different C. buqueti developmental stages, namely eggs, larvae, pupae, adult male and adult female, were used [ 35 ]. We downloaded raw data from the National Centre for Biotechnology Information (NCBI) ( https://www.ncbi.nlm.nih.gov/ ) and focussed on genes associated with the lignocellulose degradation pathway.…”

Complete mitochondrial genome of the bamboo snout beetle, Cyrotrachelus buqueti (Coleoptera: Curculionidae)

“…The bamboo snout beetle, Cyrtotrachelus buqueti Guerin-Meneville (Coleoptera: Curculionidae), is a highly destructive forest pest and distributed widely in Southeast Asia (Yang et al 2017). The larvae of C. buqueti bore into the shoots of clumping bamboo species, causing serious damage to bamboo production (Yang et al 2009).…”