3.1 | Genome resequencing and genetic variation
A total of 44 individuals from threeParascaris spp. populations of horses, zebra, donkey from Inner Mongolia and Heilongjiang of China were whole-genome sequenced (Fig. 1). We identified 4,398,519 SNPs with a genome-wide distribution of 1 SNP per 57 bp on average (Fig. S1). Genome resequencing was accomplished with an average depth of 20X (Fig. S2), average mapping rate of 98.17% and with > 90% genomic coverage of all individuals (Table S2). Currently there is a dispute over whether there are two types of horse roundworms (P. equorum orP. univalens ) or not. The BWA alignment confirmed that the all individuals were closer to P. univalens , with an average mapping rate against P. equorum of 78%, significantly lower than that against the P. univalensgenome (P <0.01) (Fig. S3a). We have counted the number of shared SNPs among the three populations, and found that 1,244,910 SNPs were shared among them. PEc has 1,055,384 unique SNPs, while PEz and PEa have only 206,419 and 65,110 respectively. This also showed the genetic difference between PEc and the other two populations. In addition, we calculated the observed heterozygosity and expected heterozygosity of individuals in populations to ensure that each population is represented (Table S3).