The cotton bollworm Helicoverpa armigera, is one of the world's major pest of agriculture, feeding on over 300 hosts in 68 plant families. Resistance cases to most insecticide classes have been reported for this insect. Management of this pest in agroecosystems relies on a better understanding of how it copes with phytochemical or synthetic toxins. We have used genome editing to knock out a cluster of nine P450 genes and show that this significantly reduces the survival rate of the insect when exposed to two classes of host plant chemicals and two classes of insecticides. Functional expression of all members of this gene cluster identified the P450 enzymes capable of metabolism of these xenobiotics. The CRISPR-Cas9-based reverse genetics approach in conjunction with in vitro metabolism can rapidly identify the contributions of insect P450s in xenobiotic detoxification and serve to identify candidate genes for insecticide resistance.

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CYP6AE gene cluster knockout in Helicoverpa armigera reveals role in detoxification of phytochemicals and insecticides.

The rapid wide-scale spread of fall armyworm (Spodoptera frugiperda) has caused serious crop losses34 globally However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood Here we report the assembly of a 39038-M chromosome-level genome of fall armyworm using Pacific Bioscience (PacBio) and Hi-C sequencing technologies with scaffold N50 of 127 M consisting of 22260 annotated protein-coding genes Genome-wide resequencing of 103 samples from 16 provinces in China revealed that the fall armyworm population comprises a complex inter-strain hybrid, mainly with the corn-strain genetic background and less of the rice-strain, which highlights the inaccuracy of strain identification using mitochondrial or Triosephosphate isomerase (Tpi) genes Analysis of genes related to pesticide- and Bt-resistance showed that the risk of fall armyworm developing resistance to conventional pesticides is very high Laboratory bioassay results showed that insects invading China carry resistance to organophosphate and pyrethroid pesticides, but are sensitive to genetically modified maize expressing Bacillus thuringiensis (Bt) toxins Cry1Ab in field experiments Additionally, two mitochondrial fragments are inserted into the nuclear genome, and the insertion event occurred after the differentiation of the two strains This study represents a valuable advance toward improving management strategies for fall armyworm

https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13219

Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China.

The fall armyworm (Spodoptera frugiperda) is a lepidopteran insect pest that causes huge economic losses. This notorious insect pest has rapidly spread over the world in the past few years. However, the mechanisms of rapid dispersal are not well understood. Here, we report a chromosome-level assembled genome of the fall armyworm, named the ZJ-version, using PacBio and Hi-C technology. The sequenced individual was a female collected from the Zhejiang province of China and had high heterozygosity. The assembled genome size of ZJ-version was 486 Mb, containing 361 contigs with an N50 of 1.13 Mb. Hi-C scaffolding further assembled the genome into 31 chromosomes and a portion of W chromosome, representing 97.4% of all contigs and resulted in a chromosome-level genome with scaffold N50 of 16.3 Mb. The sex chromosomes were identified by genome resequencing of a single male pupa and a single female pupa. About 28% of the genome was annotated as repeat sequences, and 22,623 protein-coding genes were identified. Comparative genomics revealed the expansion of the detoxification-associated gene families, chemoreception-associated gene families, nutrition metabolism and transport system gene families in the fall armyworm. Transcriptomic and phylogenetic analyses focused on these gene families revealed the potential roles of the genes in polyphagia and invasion of fall armyworm. The high-quality of the fall armyworm genome provides an important genomic resource for further explorations of the mechanisms of polyphagia and insecticide resistance, as well as for pest management of fall armyworm.

The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion

Biology, invasion and management of the agricultural invader: Fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae)

The brown planthopper Nilaparvata lugens, white-backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome-level genome resources has hindered in-depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome-level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re-sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex-linked genes, and all chromosomes showed high synteny. The chromosome-level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies.

Chromosomal-level genomes of three rice planthoppers provide new insights into sex chromosome evolution

The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion.

/pdf/a-chromosome-level-genome-assembly-of-cydia-pomonella-gm0en3q9ek.pdf

A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

Glutathione S-transferases (GSTs) play a major role in the detoxification of insecticides and the protection against oxidative damage caused by ROS (reactive oxygen species). The bird cherry-oat aphid, Rhopalosiphum padi (L.), is a major crop pest worldwide. Chemical insecticides are currently used to control aphids, but insecticide resistance is an evolutionary issue for aphid control. In this research, we identified and cloned the full-length cDNA of a theta-class GST gene (RpGSTT1) from R. padi, which contains 702 bp open reading frame encoding 233 amino acids. RpGSTT1 was clustered together with theta classe of insect GSTs in the phylogenetic tree. Effect of insecticide exposure on the GST enzyme activity was investigated in vivo. After affinity purification, the recombinant RpGSTT1 protein was able to catalyze the conjugation of 1-chloro-2, 4-dinitrobenzene (CDNB). A disc diffusion assay showed that the RpGSTT1 can increase resistance to cumene hydroperoxide-induced oxidative stress. In addition, the purified recombinant RpGSTT1 protected super-coiled DNA from oxidative damage. By quantitative PCR, The relative expression level of RpGSTT1 in the aphid was highly up-regulated after 12 h exposure to β-cypermethrin, isoprocarb, malathion and sulfoxaflor, respectively. To our knowledge, RpGSTT1 is the first theta class of GST gene reported in bird cherry-oat aphid. Our findings indicate that RpGSTT1 may be involved in insecticide detoxification in R. padi. 

A novel theta-class glutathione S-transferase gene in Rhopalosiphum padi (L.) (Hemiptera: Aphididae): identification, recombinant protein expression and function analyses of RpGSTT1

Rhopalosiphum padi is an important global wheat pest. The pyrethroid insecticide bifenthrin is widely used in the control R. padi. We explored the resistance potential, cross-resistance, adaptive costs, and resistance mechanism of R. padi to bifenthrin using a bifenthrin-resistant strain (Rp-BIF) established in laboratory. The Rp-BIF strain developed extremely high resistance against bifenthrin (1033.036-fold). Cross-resistance analyses showed that the Rp-BIF strain had an extremely high level of cross-resistance to deltamethrin (974.483-fold), moderate levels of cross-resistance to chlorfenapyr (34.051-fold), isoprocarb (27.415-fold), imidacloprid (14.819-fold), and thiamethoxam (11.228-fold), whereas negative cross-resistance was observed to chlorpyrifos (0.379-fold). The enzymatic activity results suggested that P450 played an important role in bifenthrin resistance. A super-kdr mutation (M918L) of voltage-gated sodium channel (VGSC) was found in the bifenthrin-resistant individuals. When compared with the susceptible strain (Rp-SS), the Rp-BIF strain was significantly inferior in multiple life table parameters, exhibiting a relative fitness of 0.69. Our toxicological and biochemical studies indicated that multiple mechanisms of resistance might be involved in the resistance trait. Our results provide insight into the bifenthrin resistance of R. padi and can contribute to improve management of bifenthrin-resistant R. padi in the field.

Lang Liu

Papers

A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance

A novel theta-class glutathione S-transferase gene in Rhopalosiphum padi (L.) (Hemiptera: Aphididae): identification, recombinant protein expression and function analyses of RpGSTT1

Characterization and fitness cost of bifenthrin resistance in Rhopalosiphum padi (Hemiptera: Aphididae).