Whole genome sequencing and genetic evolution analysis of the spongy moth reveal potential genetic structures and hidden subspecies patterns

PacBio, high-throughput chromosome conformation capture (Hi-C), and third-generation transcriptome (ONT) were used to sequence and assemble and annotate the gypsy moth at the chromosome level. Subsequently, a orthologous genome was constructed and Bayesian loose molecular clock method was used to estimate the neutral evolution rate and species differentiation time using MCMCTREE program. Furthermore, SLAF Seq sequencing was performed on 26 regions of the global distribution area of the gypsy moth, resulting in 259193 SNPs. Genetic diversity analysis was conducted using filtered loci. The results showed that the total size of the genome draft was 1.9 Gb, containing two complete sets of haplotypes. The contig N50 reached 35 Mb, with 8 gaps and good continuity. 30744 and 15675 gene descriptions were obtained from Nr and SwissProt, accounting for 93.08 and 47.46% of the total number of genes, respectively. Comparative genomics analysis shows that, except for Drosophila melanogaster as an outgroup, all other Lepidoptera species cluster together. The L. dispar japonica and L. dispar asiatica of spongy moth clustered into one branch and differentiated 3.9 million years ago (2.3Mya-6.1Mya). The southwest population of gypsy moth formed their sisters group and differentiated about 5.8 million years ago (3.5Mya-8.7Mya). 299 and 1120 expanded gene families, 991 and 1576 contracted gene families, and 796 and 1056 rapidly evolving gene families were discovered in the Southwest and Northern population. The genetic structure indicates that apart from the widely recognized three subspecies, the southwest population of China has independently evolved into one subspecies. Subsequently, morphological observations confirmed this conclusion.