Fig 1.
The life cycles of S. stercoralis and N. americanus.
(A) The life cycle of Strongyloides stercoralis. The numbers refer to the numbers of the developmental options in the description of the life cycle in the text. This figure was reproduced from [50] under the creative commons license. Notice that auto infective iL3s are not normally observed in naturally deposited feces and were therefore not detectable with the methods used in this study. (B) The life cycle of N. americnaus.
Table 1.
Primers and annealing temperatures for SSU, ITS rDNA and cox1 amplifications and sequencing.
Fig 2.
Cox1 gene tree of different hookworm isolates.
Maximum likelihood tree based on 670 bp of the mitochondrial cox1 gene of the hookworms isolated in this study and selected published sequences. The reference sequence AJ417719 originates from the Zhejiang Province, China [72]. The scale bar represents 0.02 substitutions per site. The boot strap values represent 1000 boot strapping repetitions. The labels are composed as follows: [author of the reference] [haplotypes names according to this reference] [host the isolate was derived from] [country the isolate was isolated from] (accession number). Samples newly isolated in this study are underlaid in red. The clade and species nomenclature on the right is according to [40].
Fig 3.
Cox1 gene tree of different S. stercoralis isolates.
Maximum likelihood tree based on 552 bp of the mitochondrial cox1 gene. Shown are the three newly identified (red box) and selected published S. stercoralis haplotypes representing the major phylogenetic groups described in recent S. stercoralis cox1 phylogenies [6, 49, 50, 73]. The scale bar represents 0.02 substitutions per site. The boot strap values represent 1000 boot strapping repetitions. The labels are composed as follows: [author of the reference] [haplotypes names according to this reference] [host the isolate was derived from] [country the isolate was isolated from] (accession number). The two columns on the right indicate the SSU HVR-I and HVR-IV haplotypes found among the worm individuals of the respective cox1 haplotype.
Table 2.
The SSU HVR-I and HVR-IV polymorphisms of S. stercoralis.
Table 3.
SSU HVR-I and HVR-IV genotypes of individual S. stercoralis.
Table 4.
Combinations of SSU HVR-I and HVR-IV haplotypes.
Fig 4.
Population structure of S. stercoralis.
(A) Phylogenetic relationships between the Chinese and selected S. stercoralis samples are visualized as a neighbor-joining tree that was calculated from 1180 concatenated variant sites that were genotyped as homozygous in all samples. (B) Principal component analysis was performed on 910 homozygous and heterozygous SNPs that could be genotyped in all samples. (C) Principal component analysis without the reference strain. (D) Nucleotide diversity (π) was calculated from homozygous SNPs as the mean fraction of nucleotide differences in pairwise comparisons within and between populations. The heatmap shows the negative logarithm (base 10) of π. Cn: China; Kh: Cambodia; MyHTB: Myanmar; Rk: Japan; Ref: US-derived reference laboratory strain PV001. For Cn and Kh all but three (very low read coverage) whole genome sequences determined for this study and for [50] were included. For MyHTB and Rk, we selected samples representing one outlier (Rk9-11) and the two clusters in Fig 5 of [54]. Selection within the clusters was random.
Fig 5.
Genomic heterozygosity of individual S. stercoralis.
The heterozygosity on the autosomes is plotted against the heterozygosity on the X chromosome for S. stercoralis individuals from different geographical locations. Cn: China; Kh: Cambodia; MyHTB: Myanmar; Rk: Japan; Ref: US-derived reference laboratory strain PV001. All samples in Fig 4 that fulfilled the read coverage criteria described in Materials and Methods were included in this analysis. The samples from Cn represent four different hosts from the village, two hospital patients and all three cox1 haplotypes (c.f. S4 file).
Fig 6.
The heterozygosity was derived from ancestral polymorphisms.
(A) The frequency of heterozygous calls in the Chinese population was quantified and compared to a neutral expectation of derived allele frequencies under a genetic drift model (1/k where k is the number of samples (dashed line) [66, 77]. (B) The frequency of the non-reference alleles derived from (A) was quantified in the Cambodian population. Large fractions of these alleles are fixed in Cambodian population (“fixed”) and the other large fraction of alleles is not found in Cambodian population (“not present”). The numbers of nonsynonymous variants in the “not present” and “fixed” group are shown in pie charts.