Matsumurasca onukii (Matsuda, 1952), one of the dominant pests in major tea production areas in Asia, currently is known to occur in Japan, Vietnam, and China, and severely threatens tea production, quality, and international export trade. To elucidate the population genetic structure of this species, 1633 single nucleotide polymorphisms (SNPs) and 18 microsatellite markers (SSRs) were used to genotype samples from 27 sites representing 18 geographical populations distributed throughout the known range of the species in East Asia. Analyses of both SNPs and SSRs showed that M. onukii populations in Yunnan exhibit high genetic differentiation and structure compared to other populations. The Kagoshima (JJ) and Shizuoka (JS) populations from Japan were separated from populations from China by SNPs but clustered with Jinhua (JH), Yingde (YD), Guilin (GL), Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY) and Zunyi (ZY) tea areas in China and the Vietnamese Vinh Phuc (VN) population based on SSR data. On the contrary, CT, CY, ZY, and Shaanxi (SX) populations clustered together based on SNPs, but were separated by SSRs. Both marker datasets identified significant geographic differentiation among the 18 populations. Various environmental and anthropogenic factors, including the geographical barriers to migration, human transport of hosts (Camellia sinesis (L.) O. Kuntze), and adaptability of M. onukii to various climatic zones possibly account for the rapid spread of this pest in Asia. The results demonstrate that SNPs from high-throughput genotyping data can be used to reveal subtle genetic substructure at broad scales in r-strategist insects.

Genotype table for 18 microsatellites generated using AFLP of sequences containing repeats (FIASCO). Each row is a microsatellite locus; each column starting with the second is an M. onukii individual. For these diploid markers, individuals have two alleles per locus. Missing data (e.g. due to low reads) are indicated by "000". For each locus, haplotypes are uniquely labeled with numbers (genotyping by automated capillary electrophoresis).

Genotype table for 1633 SNPs.  Associated raw sequence data have been deposited to the NCBI Sequence Read Archive (BioProject ID: PRJNA799739).

Genotypic data obtained by 18 microsatellite markers was submitted in Genpop format.

Genotypic data obtained by 1633 microsatellite markers was submitted in .vcf.