Study On Population Evolution Of Ascaris Lumbricoides And Ascaris Suum Based On Genome Resequencing

Ascaris lumbricoides and Ascaris suum are parasitic nematodes that mainly parasited in small intestine of people and pigs,respectively,which are easy to cause ascariasis.It seriously endangers human health.It also causes huge economic losses to the pig industry.Therefore,many countries attach great importance to the prevention and control of human and animal ascariasis.Comparative analysis on the morphological,physiological and biochemical,cellular immune and molecular biological between A.lumbricoides and A.suum indicated that they had similar morphological,similar genetic structures and occasional cross-infection.As a result,the taxonomic problem of A.lumbricoides and A.suum has been controversial.Most studies on molecular systematics and molecular genetic of A.lumbricoides and A.suum in the past were based on molecular markers such as mitochondria or microsatellites,which have not been reported at the genome level.This study analyzed population differences and genetic differentiation between A.lumbricoides and A.suum based on genome-wide sequencing for the first time,mitochondrial phylogenomics of Ascaris and developed microsatellite molecular markers based on genome of A.suum.It will provide a basis for further development of genetic,molecular epidemiology and classification and identification of A.lumbricoides and A.suum populations.The main results of this study are as follows:1.The whole genomes were resequenced of A.lumbricoides and A.suum populations by HeseqXten sequencing platform.After quality control,134.085 Gb of high-quality data were obtained.A total of 6,525,078 SNPs and 4,260,867 SNPs were detected in A.lumbricoides and A.suum,respectively.Phylogenetic tree,principal component analysis and poulation genetic structure showed obvious genetic differentiation between A.lumbricoides and A.suum.Linkage disequilibrium analysis found that A.lumbricoides population was more primitive than A.suum population.2.Selective elimination analysis showed that 160 and 139 candidate regions were screened for A.lumbricoides and A.suum respectively.The selected regions were analysed by GO enrichment and KEGG pathway analysis.A.lumbricoides population had no significant enrichment in the GO term and 2 KEGG pathways significantly enriched including the RNA degradation pathway and the tyrosine metabolic pathway.There were 5 GO entries and 1 KEGG pathway that were significantly enriched in the A.suum population.The significantly enriched pathway was alanine,aspartic acid and glutamate signaling pathways.3.Demographic history of Ascaris populations revealed A.lumbricoides and A.suum had similar effective population size change trend in different historical periods.The Ascaris populations peaked around 1 million years ago and then began to decline.In the last glacial period,they dropped to a historical low and continued until the last glacial maximum.This phenomenon may be associated with cold climate at that time.4.We screened 682 microsatellite loci from the 273Mb genome of the A.suum.And 104 of them were selected for primer design and polymorphism testing.Twenty-five microsatellite loci that had polymorphisms and resulted in stable amplification were obtained.The number of alleles per locus ranged from 2 to 25;the observed heterozygosity?H_O?and expected heterozygosity?H_E?were 0 to 1 and 0.042 to 0.945,respectively;and the polymorphism information content?PIC?was 0.040 to 0.921,with20 pairs showing higher levels of polymorphisms.The frequency of null alleles?F?and inbred coefficient(F_IS)ranged from 0 to 0.2933 and-0.1985 to 1,indicating loss of heterozygotes.Among the 25 pairs of microsatellite molecular markers,fifteen pairs of microsatellite markers conform to Hardy-Weinberg equilibrium?HWE?,and 10 loci showed more or less deviations from HWE.These loci can also be stably amplified in A.lumbricoides.5.By sequencing the mitochondrial genome of pure-bred human Ascaris,pure-bred pig Ascaris,and hybrized Ascaris,they including 36 genes?lack of atp8?which were 12 protein-coding genes,2 rRNA genes and 22 tRNA genes.And all genes were on the H chain,ATT and TTG were used for starting codons of protein-coding genes,and TAA and TAG were used for stoping codons.The distribution of the bases showed obvious AT bias.6.Phylogenetic trees based on whole mitochondrial genome and cox1 sequences of pure-bred human Ascaris,pure-bred pig Ascaris,and hybrized Ascaris showed they had the similar topological structure.As shown in the phylogenetic trees,three clusters?A,B,and C?had distinct phylogenetic relationship.The newly sequenced Ascaris populations genomes gathered inside cluster B.The differences of sequence between individuals were small.