Evolutionary genomics of three agricultural pest moths reveals rapid evolution of host adaptation and immune-related genes

Abstract

Background Understanding the genotype of pest species provides an important baseline for designing integrated pest management (IPM) strategies. Recently developed long-read sequence technologies make it possible to compare genomic features of nonmodel pest species to disclose the evolutionary path underlying the pest species profiles. Here we sequenced and assembled genomes for 3 agricultural pest gelechiid moths: Phthorimaea absoluta (tomato leafminer), Keiferia lycopersicella (tomato pinworm), and Scrobipalpa atriplicella (goosefoot groundling moth). We also compared genomes of tomato leafminer and tomato pinworm with published genomes of Phthorimaea operculella and Pectinophora gossypiella to investigate the gene family evolution related to the pest species profiles. Results We found that the 3 solanaceous feeding species, P. absoluta, K. lycopersicella, and P. operculella, are clustered together. Gene family evolution analyses with the 4 species show clear gene family expansions on host plant–associated genes for the 3 solanaceous feeding species. These genes are involved in host compound sensing (e.g., gustatory receptors), detoxification (e.g., ABC transporter C family, cytochrome P450, glucose-methanol-choline oxidoreductase, insect cuticle proteins, and UDP-glucuronosyl), and digestion (e.g., serine proteases and peptidase family S1). A gene ontology enrichment analysis of rapid evolving genes also suggests enriched functions in host sensing and immunity. Conclusions Our results of family evolution analyses indicate that host plant adaptation and pathogen defense could be important drivers in species diversification among gelechiid moths.

The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics

“…The use of genomic data has revolutionized our understanding of the natural world. In particular, understanding genomic phenomena such as the expansion and contraction of gene families, which comprise a set of genes that tend to exhibit functional similarity [ 25 , 26 ], can provide relevant insights into functional aspects of organisms [ 27 , 28 ]. For example, it has been demonstrated that the genomes of the German cockroach and house fly, among all sequenced insects, have the largest repertoires of sensory receptors within the insect pickpocket gene family, which are responsible for detecting certain environmental stimuli such as water and salt [ 29 ].…”