Using Next-Generation Sequencing to Detect Differential Expression Genes in Bradysia odoriphaga after Exposure to Insecticides

Abstract

Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive. Insecticides are used widely and frequently to control B. odoriphaga in China. However, the performance of the insecticides chlorpyrifos and clothianidin in controlling the Chinese chive maggot is quite different. Using next generation sequencing technology, different expression unigenes (DEUs) in B. odoriphaga were detected after treatment with chlorpyrifos and clothianidin for 6 and 48 h in comparison with control. The number of DEUs ranged between 703 and 1161 after insecticide treatment. In these DEUs, 370–863 unigenes can be classified into 41–46 categories of gene ontology (GO), and 354–658 DEUs can be mapped into 987–1623 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expressions of DEUs related to insecticide-metabolism-related genes were analyzed. The cytochrome P450-like unigene group was the largest group in DEUs. Most glutathione S-transferase-like unigenes were down-regulated and most sodium channel-like unigenes were up-regulated after insecticide treatment. Finally, 14 insecticide-metabolism-related unigenes were chosen to confirm the relative expression in each treatment by quantitative Real Time Polymerase Chain Reaction (qRT-PCR). The results of qRT-PCR and RNA Sequencing (RNA-Seq) are fairly well-established. Our results demonstrate that a next-generation sequencing tool facilitates the identification of insecticide-metabolism-related genes and the illustration of the insecticide mechanisms of chlorpyrifos and clothianidin.

Transcriptome Analysis and Identification of Insecticide Tolerance-Related Genes after Exposure to Insecticide in Sitobion avenae

“…After 36 h of insecticide treatment, they may have significantly up-or downregulated. In B. odoriphaga, when samples were treated with chlorpyrifos and clothianidin for 6 h and 48 h, the number of DEUs related to insecticide tolerance was not much different, and the majority of insecticide tolerance-related unigenes responded in 6 h; however, there were still some insecticide tolerance-related unigenes that responded in 48 h [6], which was similar to the results of the current study. Therefore, the results of this study may indicate that exposure to insecticides for 3 h does not lead to a great increase in tolerance-related unigenes.…”

“…Trypsin-related genes accounted for a large group of DEUs in B. oriphaga under insecticide stress [6] and were found to be highly expressed in C. pipiens pallens deltamethrin-resistant strains [42]. Following exposure to triazophos, imidacloprid, chlorpyrifos, and abamectin, trypsin expression was upregulated in Sodatella furcifera [43].…”

“…However, studies of the insecticide detoxification of grain aphids arelimited. RNA-Seq is now a common method used to analyze gene expression [4], and this method has been used to identify insecticide metabolism-related genes in several species, including Aedes aegypti [5], Bradysia odoriphaga [6], and Plutella xylostella [7]. There are no transcriptome analyses about S. avenae under insecticide pressure that have been conducted to date [8,9].…”

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

“…The brief analytical pipeline for both platforms including initial quality check, reads filtering, mapping to Arabidopsis genome and subsequent transcriptome-related analysis following the standard procedures has been published previously (Fig. 1 ) [ 27 , 28 ]. The quality assessment and platform comparison will be discussed in the forthcoming sections.…”

“…The bioinformatic pipeline was performed as described previously with minor modifications [ 27 , 28 ]. Raw sequencing reads were filtered to get clean reads by using SOAPnuke (v1.5.2, parameters -l 15, -q 0.2, -n 0.05) ( https://github.com/BGI-flexlab/SOAPnuke ).…”