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

Haoliang Chen,Guangling Zhang,Farman Ali,Minghui Xie,Weihua Su,Lulu Lin

doi:10.3390/ijms18112445

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.

Highlights

Chinese chive, Allium tuberosum Rottler ex Sprengel (Asparagales: Amaryllidaceae) is considered to be an important vegetable in north China, because it is the main stuffing for dumplings
De novo transcriptome sequencing of all stages of B. odoriphaga generated 34,154 unigenes, with a total length of 38,551,589 bp, a mean length of 1128 bp and an N50 (50% of the total assembled sequence was contained in contigs of this length or longer) of 1984 bp
A total of 20,058 unigenes were annotated against the National Center for Biotechnology Information (NCBI) NR protein database, 5280 in gene ontology (GO) function categories, and 15,910 unigenes were mapped onto the canonical pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG)

Summary

Introduction

Allium tuberosum Rottler ex Sprengel (Asparagales: Amaryllidaceae) is considered to be an important vegetable in north China, because it is the main stuffing for dumplings. In north China, B. odoriphaga can cause heavy losses to the production of Chinese chive or even ruin the whole crop if not treated with insecticides [3]. Chlorpyrifos, which we tested, has been widely used in Anhui province to control the Chinese chive maggot, whereas clothianidin has not been used against B. odoriphaga before. The widespread frequent application of chemical insecticides (e.g., organophosphates, and neonicotinoids) is the most prevalent management strategy used against B. odoriphaga when planting the Chinese chive in China. This has led to an excessive use of insecticides resulting in environmental pollution and high residues on marketed chives

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Conclusion