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Power RI, Doyle SR, Šlapeta J. Whole genome amplification and sequencing of individual Dirofilaria immitis microfilariae. Exp Parasitol 2024; 263-264:108806. [PMID: 39009178 DOI: 10.1016/j.exppara.2024.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
Dirofilaria immitis is a filarial parasitic nematode of veterinary significance. With the emergence of drug-resistant isolates in the USA, it is imperative to determine the likelihood of resistance occurring in other regions of the world. One approach is to conduct population genetic studies across an extensive geographical range, and to sequence the genomes of individual worms to understand genome-wide genetic variation associated with resistance. The immature life stages of D. immitis found in the host blood are more accessible and less invasive to sample compared to extracting adult stages from the host heart. To assess the use of immature life stages for population genetic analyses, we have performed whole genome amplification and whole-genome sequencing on nine (n = 9) individual D. immitis microfilaria samples isolated from dog blood. On average, less than 1% of mapped reads aligned to each D. immitis genome (nuclear, mitochondrial, and Wolbachia endosymbiont). For the dog genome, an average of over 99% of mapped reads aligned to the nuclear genome and less than 1% aligned to the mitochondrial genome. The average coverage for all D. immitis genomes and the dog nuclear genome was less than 1, while the dog mitochondrial genome had an average coverage of 2.87. The overwhelming proportion of sequencing reads mapping to the dog host genome can be attributed to residual dog blood cells in the microfilariae samples. These results demonstrate the challenges of conducting genome-wide studies on individual immature parasite life stages, particularly in the presence of extraneous host DNA.
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Affiliation(s)
- Rosemonde I Power
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, 2006, Australia
| | - Stephen R Doyle
- Wellcome Sanger Institute, Cambridgeshire, CB10 1SA, United Kingdom
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales, 2006, Australia; Sydney Infectious Diseases Institute, The University of Sydney, New South Wales, 2006, Australia.
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Gandasegui J, Power RI, Curry E, Lau DCW, O'Neill CM, Wolstenholme A, Prichard R, Šlapeta J, Doyle SR. Genome structure and population genomics of the canine heartworm Dirofilaria immitis. Int J Parasitol 2024; 54:89-98. [PMID: 37652224 DOI: 10.1016/j.ijpara.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
The heartworm, Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources of D. immitis to enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly for D. immitis (ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes of Brugia malayi and Onchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one sex-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32 D. immitis samples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between-population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped single nucleotide polymorphisms previously associated with macrocyclic lactone resistance in the new genome assembly, revealing the physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly for D. immitis now allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment.
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Affiliation(s)
- Javier Gandasegui
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - University of Barcelona, Barcelona, Spain.
| | - Rosemonde I Power
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Emily Curry
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, Canada.
| | - Daisy Ching-Wai Lau
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Connor M O'Neill
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
| | - Adrian Wolstenholme
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
| | - Roger Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, Canada.
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, Australia.
| | - Stephen R Doyle
- Wellcome Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom.
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Stevens L, Kieninger M, Chan B, Wood JMD, Gonzalez de la Rosa P, Allen J, Blaxter M. The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes. PLoS Genet 2024; 20:e1011116. [PMID: 38227589 PMCID: PMC10817185 DOI: 10.1371/journal.pgen.1011116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/26/2024] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Brian Chan
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | | | | | - Judith Allen
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
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Gomes-de-Sá S, Santos-Silva S, Moreira ADS, Barradas PF, Amorim I, Cardoso L, Mesquita JR. Assessment of the circulation of Dirofilaria immitis in dogs from northern Portugal through combined analysis of antigens, DNA and parasite forms in blood. Acta Trop 2023; 239:106799. [PMID: 36572345 DOI: 10.1016/j.actatropica.2022.106799] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022]
Abstract
Dirofilariasis is a vector-borne disease frequent in many countries. Not only infected dogs, but also cats and wild canids (including wolves and foxes), represent important sources of infection for mosquitoes, which are the pathogen vectors. The disease is endemic in Mediterranean countries with increasing incidence in Italy, France, Greece and Spain, but limited epidemiological data is available from Portugal regarding its distribution and impact. Aiming to clarify this, canine whole blood samples (n = 244) from the north of Portugal were tested for Dirofilaria spp. antigens by use of a commercial rapid immunomigration test. Polymerase chain reaction (PCR) and the modified Knott test were also used to assess the presence of microfilariae. Results were also compared to assess the performance of each test used. Of the 244 animals tested, 118 (48.4%) were positive for Dirofilaria immitis (heartworm) in the serological adult worm rapid antigen detection test, and 36 (14.8%) had circulating microfilariae, identified as D. immitis. A combined positivity of 51.6% (126/244) was found. Results indicate that the risk of exposure to D. immitis in dogs is high in this region of Portugal, and that prophylaxis against the parasite is advisable to decrease the occurrence of canine infection and disease. The present study highlights the diagnostic value of serological and molecular tests in determining the prevalence of D. immitis.
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Affiliation(s)
- Sónia Gomes-de-Sá
- ICBAS - School of Medicine and Biomedical Sciences, Porto University, Porto, Portugal
| | - Sérgio Santos-Silva
- ICBAS - School of Medicine and Biomedical Sciences, Porto University, Porto, Portugal
| | | | - Patrícia Ferreira Barradas
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Department of Sciences, CESPU, CRL, University Institute of Health Sciences (IUCS), Gandra, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Irina Amorim
- ICBAS - School of Medicine and Biomedical Sciences, Porto University, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Luís Cardoso
- Department of Veterinary Sciences, and CECAV - Animal and Veterinary Research Centre, University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Portugal
| | - João R Mesquita
- ICBAS - School of Medicine and Biomedical Sciences, Porto University, Porto, Portugal; Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal.
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