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

Abstract

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. K E Y W O R D S chromosome-level genome, comparative genomics, fall armyworm, insecticide resistance, polyphagia | 1051 XIAO et Al.

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

“…Genomes size assembled in this study fell within the scope of 246 Mb to 809 Mb of the Lepidopteran species (Triant et al, 2018). However, the size of the genome reported in the current study is larger than that of the previously assembled FAW genomes (Kakumani et al, 2014;Gouin et al, 2017;Nam et al, 2018Nam et al, , 2019Nandakumar et al, 2017;Zhang et al, 2019Zhang et al, , 2020Xiao et al, 2020) (Table 1). The extra regions of c h r 2 7 c h r 2 8 c h r2 9 ch r3 0 chr3 1 Figure 1.…”

“…(C) Synteny between FAW and Spodoptera litura genome. The gray lines reveal the genome-wide collinearity, and the red lines reveal the our FAW genome compared with that published by Xiao (Xiao et al, 2020) are evenly distributed on 31 chromosomes (Fig. S2).…”

“…In January 2019, FAW was first reported in Yunnan Province of China (Jing et al, 2019), and then rapidly spread to 13 provinces and cities (Yunnan, Guizhou, Sichuan, Chongqing, Guangxi, Guangdong, Hainan, Hunan, Hubei, Fujian, Zhejiang, Jiangxi and Henan) of China within only four months (Wu et al, 2019). With the fast dispersal rates and available suitable habitats in the southwest, central and northern regions of China, the pest had already attacked 1,366 counties (cities and districts) across 24 provinces of China until August 17, 2019 (Xiao et al, 2020). The recent FAW invasion in China has caused tremendous losses of agricultural production in the invaded regions and has become a great threat to the corn production in eastern China, the major regions of corn production in China (Li et al, 2019).…”

“…However, the FAW genomes from its cell lines or strains are fragmented without anchoring on chromosomes before the year 2019 (Gouin et al, 2017;Kakumani et al, 2014;Nam et al, 2018Nam et al, , 2019Nandakumar et al, 2017). With the advancement in genome sequencing and assembly technology, three chromosome-level genome assemblies of FAW have been published or pre-printed (Nam et al, 2019;Zhang et al, 2019Zhang et al, , 2020Xiao et al, 2020). Nevertheless, only two of them are available to the public (Xiao et al, 2020;Zhang et al, 2020).…”

“…With the advancement in genome sequencing and assembly technology, three chromosome-level genome assemblies of FAW have been published or pre-printed (Nam et al, 2019;Zhang et al, 2019Zhang et al, , 2020Xiao et al, 2020). Nevertheless, only two of them are available to the public (Xiao et al, 2020;Zhang et al, 2020). In addition, the genome sizes of the three assemblies varied dramatically from 384 to 486 Mb, even considering the sequencing technologies and potential strain differences.…”