Study on the population evolution of Ascaris lumbricoides and Ascaris suum based on whole genome resequencing.

• The whole genomes of two Ascaris populations were resequenced. • The A. lumbricoides population was more primitive than the A. suum population. • Two KEGG pathways but no GO terms were enriched in the A. lumbricoides population. • Five GO entries and one KEGG pathway were enriched in the A. suum population. • Ascaris population sizes peaked about 1 million years ago and then declined. Ascaris lumbricoides and Ascaris suum are parasitic nematodes that mainly parasitize the small intestines of people and pigs, respectively. Ascariasis seriously endangers human health and causes huge economic losses in the pig industry. A. lumbricoides and A. suum have similar morphologies and genetic structures, and occasionally these organisms cross-infect the alternate host. Therefore, their taxonomies are controversial. In this study, the whole genomes of A. lumbricoides (n = 6) and A. suum (n = 6) were resequenced using a HiSeq X Ten sequencing platform. Phylogenetic, principal component, and population structure analyses showed clear genetic differentiation between the two Ascaris populations. Linkage disequilibrium analysis indicated that the A. lumbricoides population was more primitive than the A. suum population. In the selective elimination analysis, 160 and 139 candidate regions were screened in A. lumbricoides and A. suum , respectively, and the selected regions were analyzed by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The A. lumbricoides population had no significant enrichment in GO terms, but two KEGG pathways, the RNA degradation and tyrosine metabolism pathways, were significantly enriched. Five GO entries and one KEGG pathway, the alanine, aspartate, and glutamate metabolism signaling pathway, were significantly enriched in the A. suum population. An analysis of the demographic histories of Ascaris populations revealed that A. lumbricoides and A. suum had similar trends in effective population size in different historical periods. Ascaris populations peaked about 1 million years ago and then began to decline. In the last glacial period, they dropped to a historical low and continued at this level until the last glacial maximum. This phenomenon may be associated with the cold climate at that time. This study provides new information on the genetic differentiation, evolutionary relationships, gene functional enrichment, and population dynamics of Ascaris populations, with implications for host differences, evolution, and classification of A. lumbricoides and A. suum. [ABSTRACT FROM AUTHOR]