Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions †
Abstract
1. Introduction
2. Results
2.1. Chromosome-Contiguous Genome for A. duodenale
2.2. The Annotated Genome
2.3. Genome Comparisons Between A. duodenale and N. americanus
2.4. The Secretome of A. duodenale
2.5. Conserved Single-Copy Genes Associate with Critical Functions in Nerves, Gap Junction Channel or Pore Activities, Oxidative Phosphorylation, or Thermogenesis
2.6. Structural Characterisation of ES Proteins Encoded by Aduo1G00000016964 and Aduo1G00000006435 and Their Association with Host Proteins
3. Discussion
4. Materials and Methods
4.1. DNA Isolation
4.2. DNA Sequencing
4.3. RNA Sequencing
4.4. Genome Survey and Assembly
4.5. Prediction and Functional Annotation of Protein-Coding Genes
4.6. Synteny and Genome Comparisons
4.7. Identification of Invariable Gene Sets, Inference of Essentiality, and Biological Pathway/Process Associations
4.8. Identification and Annotation of Excretory/Secretory (ES) Proteins
4.9. Structural Characterisation of ES Proteins Inferred for eSCOs, and In Silico Interactions with the Human Proteome Employing Machine Learning and Omic Data
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome Features | Ancylostoma duodenale (This Study) | Necator americanus (GCF_031761385.1) d |
---|---|---|
Genome size (bp) | 319,205,898 | 234,457,255 |
Number of chromosomes | 6 | 6 |
Number of scaffolds | 14 | 38 |
Largest chromosome (bp) | 54,937,347 | 42,005,516 |
N50 | 56,497,455 | 38,919,484 |
GC content | 42.95% | 40.09% |
Ns (gaps) a | 59,000 | 209,725 |
Number of gene models | 20,015 | 26,579 |
BUSCO—genome (c; s; d; f; m) b | 96.1; 93.9; 2.2; 2.4; 1.5 | 96.7; 95.9; 0.8; 2.1; 1.1 |
BUSCO—proteome (c; s; d; f; m) b | 94.1; 91.1; 3.0; 2.7; 3.3 | 94.2; 93.1; 1.1; 1.2; 4.6 |
OMark—proteome (cs; ics; ct; uk) c | 69.6; 6.5; 0; 24.0 | 65.7; 4.7; 0; 29.6 |
A. duodenale Gene | C. elegans Orthologue | N. americanus Homologue (NCBI) | ES Protein | Transcriptomic Evidence in A. duodenale | ES Proteomic Evidence in A. duodenale | Functional Annotation (EggNOG; Pfam; KEGG) | Predicted Structure | Biological Context |
---|---|---|---|---|---|---|---|---|
Aduo1G00000008440 | F21F3.6 | XM_064179072 | No | L3; adult (mixed sexes) | NI | NI | PL: Lysosomal membrane. | |
Aduo1G00000016964 | hot-3 | XM_013451594 | Yes | L3; adult (mixed sexes) | NI | Ly-6-related | PF: Involved in olfactory behaviour and odorant response. PL: Axon and neuronal cell body. | |
Aduo1G00000003031 | ssna-1 | XM_064198606 | No | L3; adult (mixed sexes) | NI | NI | AC: Rotenone, rifampin, psoralens. AG: atfs-1, etr-1, hsf-1. EI: ABaraapapp, ABaraapppp, anterior hypodermis, germ line, neurons. PD: Phosphorylation site. | |
Aduo1G00000003651 | T27E4.7 | XM_013440797 | No | L3; adult (mixed sexes) | NI | NI | AC: Tunicamycin, psoralens, allantoin. AG: nuo-6, cua-1, atfs-1. EI: AVF, I2L, XXXL, anchor cell, sensory neurons. | |
Aduo1G00000006435 | ZK856.7 | XM_013445741 | Yes | L3; adult (mixed sexes) | L3; adult (mixed sexes) | NI | AC: Rotenone, stavudine, zidovudine. AG: cyc-1, nuo-6, qui-1. EI: M cell, accessory cell, intestine, muscle cell. | |
Aduo1G00000011445 | R12H7.1 | XM_013444081 | No | L3; adult (mixed sexes) | NI | Gap junctions (component); innexin; K22037 | EI: Anchor cell, muscle cell, neurons, phasmid sheath cell, somatic nervous system. PF: Actin filament binding, gap junction channel activity; involved in monoatomic ion transmembrane transport, positive regulation of locomotion. PL: Gap junction. | |
Aduo1G00000012651 | pfn-2 | XM_013442503 | No | L3; adult (mixed sexes) | NI | Profilin; K05759 | EI: Pharynx, spermatheca. PF: Actin monomer binding, muscle thin filament assembly. PL: Cell cortex. |
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Young, N.D.; Zheng, Y.; Sumanam, S.B.; Wang, T.; Song, J.; Chang, B.C.H.; Gasser, R.B. Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions. Int. J. Mol. Sci. 2025, 26, 5576. https://doi.org/10.3390/ijms26125576
Young ND, Zheng Y, Sumanam SB, Wang T, Song J, Chang BCH, Gasser RB. Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions. International Journal of Molecular Sciences. 2025; 26(12):5576. https://doi.org/10.3390/ijms26125576
Chicago/Turabian StyleYoung, Neil D., Yuanting Zheng, Sunita B. Sumanam, Tao Wang, Jiangning Song, Bill C. H. Chang, and Robin B. Gasser. 2025. "Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions" International Journal of Molecular Sciences 26, no. 12: 5576. https://doi.org/10.3390/ijms26125576
APA StyleYoung, N. D., Zheng, Y., Sumanam, S. B., Wang, T., Song, J., Chang, B. C. H., & Gasser, R. B. (2025). Chromosome-Contiguous Ancylostoma duodenale Reference Genome from a Single Archived Specimen Elucidates Human Hookworm Biology and Host–Parasite Interactions. International Journal of Molecular Sciences, 26(12), 5576. https://doi.org/10.3390/ijms26125576