The evolution of parasites is often directly affected by the host’s environment or behavior. Studies on the evolution of the same parasites in different hosts are extremely attractive and highly relevant to our understanding of divergence and speciation. Here we analyzed the genetic variation of Equus roundworm populations in different hosts (horses, zebras and donkeys), and presented the first molecular evidence of divergence in Equus roundworms (Parascaris univalens). At the genetic level, Equus roundworms were mainly separated into two clades (Horse-derived and Zebra & Donkey-derived). This divergence began at 600-1500 years ago, which interestingly coincided with the domestication history of horses. We found that compared with horse-derived roundworms, most of the key enzymes related to glycolysis were under strong positive selection in zebra & donkey-derived roundworms, indicating that the evolution of the metabolic level was one of the main reasons for the divergence. In addition, we conducted a selective scan of resistance-related genes and found that the three populations were under different degrees of selection. This prompted us to pay attention to the possible impact of drugs on divergence, not just the drug resistance. This work supports that divergence or speciation is a continuous and dynamic process, and continuous monitoring of environmental factors is conducive to further understanding the adaptive evolution of roundworms.

Helminth diseases have long been a threat to the health of humans and animals. Roundworms are important organisms for studying parasitic mechanisms, disease transmission and prevention. The study of parasites in the giant panda is of importance for understanding how roundworms adapt to the host. Here, we report a high-quality chromosome-scale genome of Baylisascaris schroederi with a genome size of 253.60 Mb and 19,262 predicted protein-coding genes. We found that gene families related to epidermal chitin synthesis and environmental information processes in the roundworm genome have expanded significantly. Furthermore, we demonstrated unique genes involved in essential amino acid metabolism in the B. schroederi genome, inferred to be essential for the adaptation to the giant panda-specific diet. In addition, under different deworming pressures, we found that four resistance-related genes (glc-1, nrf-6, bre-4 and ced-7) were under strong positive selection in a captive population. Finally, 23 known drug targets and 47 potential drug target proteins (essential homologues linked to lethal phenotypes) were identified. The genome provides a unique reference for inferring the early evolution of roundworms and their adaptation to the host. Population genetic analysis and drug sensitivity prediction provide insights revealing the impact of deworming history on population genetic structure of importance for disease prevention.

Helminth diseases have long been a threat to the health of humans and animals. Roundworms are important organisms for studying parasitic mechanisms, disease transmission and prevention. The study of parasites in the living fossil giant panda is of great significance for understanding the adaptation mechanism of roundworms to the host. Here, we report a high-quality chromosome-scale genome of Baylisascaris schroederi with a genome size of 262 Mb and 19,291 predicted protein-coding genes. We found a significant expansion of genes related to epidermal chitin synthesis and environmental information processing in roundworms genome. Furthermore, we demonstrated unique genes involved in essential amino acid metabolism in the B. schroederi genome, inferred to be essential for the adaptation to the giant panda-specific diet. In addition, under different deworming pressures, we found that four resistance-related genes (glc-1, nrf-6, bre-4 and ced-7) were under strong positive selection in captive population. Finally, 23 known drug targets and 47 potential target proteins were identified. The genome provides a unique reference for inferring the early evolution of roundworms and the mechanisms underlying adaptive. Population genetic analysis and drug prediction provide insights for revealing the impact of deworming history on population genetic structure and prevention.