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

<p>The genus <i>Spodoptera</i> (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including <i>Spodoptera frugiperda</i>, <i>Spodoptera litura</i> and <i>Spodoptera exigua</i>. To effectively develop targeted pest control strategies for diverse <i>Spodoptera</i> species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of <i>S. exigua</i>, the beet armyworm. <i>Spodoptera exigua</i> is a polyphagous herbivore that can feed from &gt; 130 host plants including several economically important crops.</p> <p>The 419 Mb beet armyworm genome was sequenced from a female <i>S. exigua</i> 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 <i>S. exigua</i> 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 <i>Spodoptera</i>-specific) upregulated during 1^st and 3^rd instar larval stages for targeted pest-outbreak management.</p> <p>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 <i>Spodoptera</i> species and reveals potential lineage-specific target genes for pest control strategies.</p>