Whole-genome resequencing of tea grey geometrid provides insights into their population structure and adaptation to tea crops.

Tea grey geometrid, Ectropis grisescens (Lepidoptera: Geometridae), is a chewing defoliator of high fecundity and gluttony, whose larvae heavily consume leaves and shoots, and consequently cause significant losses to tea crops in terms of both yield and quality. Nevertheless, a lack of population genome information has hindered previous research on the species as a tea crop pest. Here, we re-sequenced genomes of 43 tea grey geometrid individuals representing 13 distinct geographic regions and 12 individuals of its sibling species, the tea geometrid Ectropis obliqua (Lepidoptera: Geometridae), collected from four different sites in China. A genomic variation atlas of 627,569 single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 43 individuals was identified. Surprisingly, the populations of the tea grey geometrid (EG) are found to be assigned into two distinct subpopulations, EGA and EGB. The sample locations indicate that the subpopulation EGA is mainly distributed in the region of Zhejiang Province, where it co-occurred with tea geometrids (EO). The EGB subpopulation is distributed in the southern and central areas of China. Demographic history analysis has revealed fluctuations in population size of the tea grey geometrid over time, but following tea cultivation, the population size has started to stabilize. Meanwhile, the migration event analysis has uncovered a significant migration event between EGA and EO. Furthermore, genes (such as P-glycoprotein and lactase) under selection show possible metabolic adaptation of tea grey geometrid to the tea plants. These findings provide a broader foundation and additional resources for understanding the geometrid evolution and the genetic mechanisms underlying agriculturally important traits.