Genome resequencing revealed genetic differentiation and promoter variation in wax secretion genes among geographic populations of Ericerus pela

Ericerus pela is an important source of insect wax with significant economic value. Despite its adaptability to diverse climates, variations in growth and wax layer thickness existed across populations. In white wax production, E. pela sourced from the Yunnan-Guizhou Plateau served as seed insects, transported to wax-producing regions (Sichuan and Hunan) to enhance white wax secretion. Genome of males was sequenced. Genome resequencing of samples from main distribution areas and some dispersal areas found 7,012,876 SNPs and 1,114,988 InDels that predominantly distributed in intergenic region and intronic region. Phylogenetics revealed three distinct groups. Group A were populations mostly from traditional insect-producing areas; Group B were mainly populations from the wax-producing areas and other dispersal areas; Group C were dispersal populations. Evolution analyses showed group A exhibited a single origin, and maintained low Ne, slow LD decay. While group B exhibited mixed ancestral origin and showed higher Ne, rapid LD decay. ZFst values and ZHp combined analyses identified some regions on tentative pseudochromosomes 3, 6, and 7 had values exceeding threshold, and the juvenile hormone esterase, cytochrome P450 301a1 were identified. Regions on the tentative pseudochromosomes 2, 3, 5 and 6 showed significantly high XP-CLR values, and elovl, fas genes were identified in these regions. Notably, certain genomic regions in three far genes had Pi and Theta values within the top 5% values of the genome-wide distribution. Analysis of their promoters revealed 24 SNPs loci and 7 InDels, and some distributed in the core promoter, CCAAT-boxes and TATA-box in the open chromatin region of far3 gene at the stage that begin to secret wax. Considerable genetic variation was observed in gene intergenic regions. Notable genetic divergence between group A and group B of E. pela was detected based on population evolution analyses. It provided a molecular basis for selective breeding of E. pela.