Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control

The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most
infamous insect pests of cultivated plants including Spodoptera
frugiperda, Spodoptera litura and Spodoptera exigua. To effectively
develop targeted pest control strategies for diverse Spodoptera species,
genomic resources are highly desired. To this aim, we provide the genome
assembly and developmental transcriptome comprising all major life stages
of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous
herbivore that can feed from > 130 host plants including several
economically important crops. The 419 Mb beet armyworm genome was
sequenced from a female S. exigua pupa. Using a hybrid genome sequencing
approach (Nanopore long read data and Illumina short read), a high-quality
genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS,
18,477 transcripts) was generated by automatic annotation and by using
transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting
evidence. In-depth analyses of developmental stage-specific expression in
combination with gene tree analyses of identified homologous genes across
Lepidoptera genomes revealed four potential genes of interest (three of
them Spodoptera-specific) upregulated during 1st and 3rd instar larval
stages for targeted pest-outbreak management. The beet armyworm genome
sequence and developmental transcriptome covering all major developmental
stages provides critical insights into the biology of this devastating
polyphagous insect pest species with a worldwide distribution. In
addition, comparative genomic analyses across Lepidoptera significantly
advance our knowledge to further control other invasive Spodoptera species
and reveals potential lineage-specific target genes for pest control
strategies.