Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, United States
- Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, United States
- Beijing Institute of Genomics, Chinese Academy of Sciences, China
- Epidemiology Research Unit (ERU) Department of Veterinary and Animal Sciences, Northern Faculty, Scotland’s Rural College (SRUC), United Kingdom
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, United States
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
- London School of Tropical Medicine and Hygiene, United Kingdom
- Royal Veterinary College, University of London, Department of Pathobiology and Population Sciences, United Kingdom
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, United States
Figures
Figure 1 with 2 supplements
Ascaris proteome.
(A) Functional classification of the predicted proteome of A. lumbricoides (an improved proteome of Ascaris spp.), excluding proteins with unknown or uncharacterized function. (B) PCA plot based on …
Figure 1—figure supplement 1
Predicted proteome and stage-specific transcriptomes of Ascaris.
(A) Functional classification of the predicted proteome of A. lumbricoides (an improved proteome of Ascaris spp.) with the majority of proteins being unknown/uncharacterized. (B) Two-dimensional …
Figure 1—figure supplement 2
Ascaris stage-specific RNA expression heatmaps.
(A) Correlation heatmap comparing parasite transcriptomes at different life stages. (B) 1870 genes differentially expressed across the stages.
Figure 2 with 4 supplements
Phylogenetics of Ascaris spp based on mitochondrial sequences.
(A) Haplotype network based on the COl mitochondrial gene. Notches on the lines separating samples represent the number of nucleotide changes between the worms represented, details on the origins of …
Figure 2—figure supplement 1
Phylogenetic trees based on cox-1 and nad-4.
Maximum likelihood phylogenetic analyses of the (A) cox-1 and (B) nad-4 genes using RaxML under the conditions of the GTR model with nodal support values generated through 1000 bootstrap replicates. …
Figure 2—figure supplement 2
Sliding window analyses.
(A) Comparison between Kenyan samples and reference mitochondrial genomes of Ascaris lumbricoides and Ascaris suum, (B) Comparison between villages, (C) cox-1 comparison between villages. Despite …
Figure 2—figure supplement 3
Evidence of Ascaris population expansion.
The pairwise nucleotide differences between worm samples (solid line) are compared to the binomial function that would most closely represent a theoretical stable population (dotted line). …
Figure 2—figure supplement 4
Ascaris SNPs and insertion/deletions (indels) maps of representative chromosomal fragments.
An assembled 6.5 Mb Ascaris lumbricoides chromosome fragment (ALgV5R006), with the frequency of identified SNPs and indels plotted for one representative A. lumbricoides-like worm from this study …
Figure 3 with 1 supplement
Genetic diversity of the Ascaris specimens.
(A) Circos plot depicting the genetic diversity of the Ascaris specimens. Outside track (red histograms) shows the total SNP diversity across the genome (first 50 largest scaffolds) in 10 kb sliding …
Figure 3—figure supplement 1
Somy analysis of the Ascaris worm specimens.
The ploidy of the Ascaris specimens are represented in a heatmap. Ploidy was calculated by averaging the count of aligned reads in 10 kb sliding windows across the genome after reference mapping …
Figure 4 with 1 supplement
Comparative genomics and population genetic structure of Ascaris.
(A) Hierarchy phylogenetic tree of Ascaris specimens. Phylogenetic tree was constructed with genome wide SNPs (at 10x coverage) from 68 Ascaris specimens, including the A. suum reference (outgroup). …
Figure 4—figure supplement 1
Admixture clustering and current population genetic structure of Ascaris were determined.
Data analyzed with POPSICLE with an ancestral population size = 4 (A) and 8 (B) in 10 kb sliding windows as described in Figure 4E.
Figure 5
Local admixture clustering and genome wide analysis of inheritance of haploblocks of Ascaris obtained by POPSICLE (Shaik et al., 2018).
Based on ancestral population K = 6. X-axis = specimens. Red highlighted box indicates the introgression of large haplotype blocks of defined parentage among the different specimens of Ascaris in …
Figure 6 with 2 supplements
PCA plot of worms sequenced for five Kenyan villages.
Each point is color-coded by village-of-origin and plotted according to the first and second principal components, based on genome sequences. Worms from village #1 are found in each of three …
Figure 6—figure supplement 1
Plot of phylogenetic distances compared to geographic distances.
(A) For village #1 and village #5. (B) Plot of diversity versus geographical distance (Hs on left, Fst on right). Genetic distances based on cox-1 genes are plotted against the geographic distances …
Figure 6—figure supplement 2
Map of Bungoma and West Sang’alo Sub-District.
(A) Bungoma town is shown by a red marker in a map of Kenya (Google Maps). (B) This map highlights the area covered by the four study villages and the pilot study village (Ranje). The locations of …
Tables
Table 1
Ascaris germline genome assemblies.
| Features | A. lumbricoides de novo | A. lumbricoides semi-de novo* | A. lumbricoides reference-based | A. suum† (Wang et al., 2017) | A. suum† (Jex et al., 2011)§ |
|---|---|---|---|---|---|
| Assembled bases (Mb) | 269.2 | 307.9 | 296.0 | 298.0 | 272.8 |
| N50 (Mb) | 0.29 | 4.77 | 4.63 | 4.65 | 0.41 |
| N50 number | 269 | 21 | 21 | 21 | 179 |
| N90 (Mb) | 0.04 | 0.95 | 0.91 | 0.92 | 0.08 |
| N90 number | 1112 | 74 | 75 | 75 | 748 |
| Total scaffold number | 8111 | 412 | 415 | 415 | 29,831 |
| Largest scaffold length (Mb) | 1.9 | 13.9 | 13.2 | 13.4 | 3.8 |
| Protein-coding genes | 17,011‡ | 17,105‡ | 17902 | 18,025 | 18,542‡ |
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* Exhibits ~23 Mb of sequence gaps and 15.4 Mb of unplaced sequence in 4072 short contigs.
† The three A. lumbricoides assemblies constructed here are compared to the A. suum assemblies from Australia (Jex et al., 2011) and the United States (Wang et al., 2017).
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‡21–23% are only partial genes based on the annotation from A. suum (Wang et al., 2017).
§ The sample for sequencing is derived from a mixture of the germline and somatic genomes (after DNA elimination).
Table 2
Effects of host, household, village, and time point on the genetic variation of Ascaris.
| Nuclear genome phylogeny* | Mitochondrial genome phylogeny | |||||
|---|---|---|---|---|---|---|
| R† | p-value | p-adjusted (Bonferroni) | R† | p-value | Samples† | |
| Individual | 0.933 | 0.001 | 0.004 | 0.996 | 0.095 | 68 worms from 60 people |
| Household | 0.020 | 0.110 | 0.440 | 0.011 | 0.340 | 68 worms from 43 houses |
| Village | 0.052 | 0.001 | 0.004 | 0.013 | 0.335 | Five villages with 43, 17, 4, 3, and one individual each |
| Time point | 0.018 | 0.162 | 0.648 | 0.024 | 0.100 | 55 at baseline and 13 post-deworming |
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* Results based on PERMANOVA using phylogenetic distances among worms. Results were largely similar using a distance matrix generated from the PCA plot (Figure 6) and using the Multi-Response Permutation Procedure (MRPP) method (Supplementary file 9).
† Since some worms did not have metadata associated with each variable examined, and some variables were over-represented in the sample (for example, 43 of 68 worms came from a single village) the samples are specified in this column.
Additional files
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Supplementary file 1
Characteristics of genome assemblies.
Reference A. lumbricoides genomes generated as part of this study (1 and 3) are compared with reference genomes for A. suum generated previously (2 and 4).
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp1-v1.xlsx
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Supplementary file 2
Proteome annotation.
While ~94.6% of the genes can be transferred to both genomes, over 20% of the transferred genes are only partial matches and are fragmented supporting the view that the de novo and semi de novo A. lumbricoides assemblies are highly fragmented.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp2-v1.xlsx
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Supplementary file 3
Description of worm from which each sample was sequenced.
The sex of the worm (based on morphological identification) and the part of the worm (germline vs somatic) is listed. Some hosts donated multiple worms.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp3-v1.xlsx
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Supplementary file 4
cox-1 haplotype list.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp4-v1.xlsx
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Supplementary file 5
X4 ratio analyses of Clades A and B using complete mitochondrial genomes used to construct the phylogeny in Figure 2b.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp5-v1.docx
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Supplementary file 6
Demographic analyses using Tajima’s D and Fu’s F statistic across complete mitochondrial genomes as a detection for the signature of population expansion events.
Whether all sequences collected globally, or just sequences collected in Kenya as part of this study were examine, the Tajima’s D value was negative and significant (indicating an excess of low frequency polymorphisms) and the Fu’s Fs was positive but not significant (potentially indicating a deficiency in diversity as would be expected in populations that has recently undergone a bottle neck event).
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp6-v1.docx
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Supplementary file 7
Number of heterozygous and homozygous SNPs in each of the 68 worms from Kenya sequenced.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp7-v1.xlsx
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Supplementary file 8
Reference mitochondrion genomes.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp8-v1.xlsx
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Supplementary file 9
Supplement to Table 2 using alternative measures of phylogenetic distance.
- https://cdn.elifesciences.org/articles/61562/elife-61562-supp9-v1.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/61562/elife-61562-transrepform-v1.docx
