Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

Abstract

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.

Geographic Monitoring of Insecticide Resistance Mutations in Native and Invasive Populations of the Fall Armyworm

“…A whole-genome analysis is necessary to contrast the abundance of P450 genes between invasive and native populations, because P450 genes exist in multi-copies scattered across the genome [ 9 , 10 , 11 ]. Our whole genome analysis at a population level shows an increased copy number of P450 genes in the invasive FAW populations.…”

“…Fall armyworm (FAW, Spodoptera frugiperda, J.E.Smith) (Lepidoptera: Noctuidae: Noctuinae) is one of the most damaging pest insects, partly due to the extreme polyphagy by feeding on at least 353 species in 76 plant families, which include several economically important crops such as corn, rice, sorghum, sugarcane, cotton, and soybean [ 8 ] Genomic analyses have demonstrated a rapid expansion of detoxification genes [ 9 , 10 , 11 ], potentially associated with this extreme polyphagy by overcoming plant defense toxins from diverse plants.…”

Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes

“…Comparatively, only 38 CYPs were identified in Pediculus humanus humanus ( Lee et al, 2010 ). A previous study has examined CYPs of FAW by whole genome-wide sequencing and finally identified 152 CYP gene clusters ( Gui et al, 2020 ). These results also corroborated the ideas of Xiao et al (2020) , who discovered 169 FAW CYPs with widespread expression at different developmental stages ( Xiao et al, 2020 ).…”

FAWMine: An integrated database and analysis platform for fall armyworm genomics

“…Reads were trimmed for quality control using Trimmomatic (Bolger et al ., 2014). Clean reads were mapped to the FAW genome assembly from BGI male (Gui et al ., 2020) using HISAT2 with the default parameters (Kim et al ., 2015). Mapped reads were sorted using SAMtools and transcript expression was summarized using HTSeq (Anders et al ., 2015).…”

“…Nine genome assemblies have been reported (Kakumani et al, 2014;Nandakumar et al, 2017;Gouin et al, 2017;Zhang et al, 2019;Nam et al, 2018Nam et al, , 2019Xiao et al, 2020). Recently, we assembled two chromosome-scale genomes of male and female FAW from China with superior quality compared with other FAW assemblies reported to date (Gui et al, 2020). A series of transcriptome data sets was produced across various strains and treatments (Landais et al, 2003;Legeai et al, 2014;Kakumani et al, 2015;do Nascimento et al, 2015;Silva-Brandao et al, 2017;Orsucci et al, 2018;Chang et al, 2020).…”