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Maizels RM, Newfeld SJ. Convergent Evolution in a Murine Intestinal Parasite Rapidly Created the TGM Family of Molecular Mimics to Suppress the Host Immune Response. Genome Biol Evol 2023; 15:evad158. [PMID: 37625791 PMCID: PMC10516467 DOI: 10.1093/gbe/evad158] [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: 06/12/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
The Transforming Growth Factor-β mimic (TGM) multigene family was recently discovered in the murine intestinal parasite Heligmosomoides polygyrus. This family was shaped by an atypical set of organismal and molecular evolutionary mechanisms along its path through the adaptive landscape. The relevant mechanisms are mimicry, convergence, exon modularity, new gene origination, and gene family neofunctionalization. We begin this review with a description of the TGM family and then address two evolutionary questions: "Why were TGM proteins needed for parasite survival" and "when did the TGM family originate"? For the former, we provide a likely answer, and for the latter, we identify multiple TGM building blocks in the ruminant intestinal parasite Haemonchus contortus. We close by identifying avenues for future investigation: new biochemical data to assign functions to more family members as well as new sequenced genomes in the Trichostrongyloidea superfamily and the Heligmosomoides genus to clarify TGM origins and expansion. Continued study of TGM proteins will generate increased knowledge of Transforming Growth Factor-β signaling, host-parasite interactions, and metazoan evolutionary mechanisms.
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Affiliation(s)
- Rick M Maizels
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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2
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Reyes-Guerrero DE, Jiménez-Jacinto V, Alonso-Morales RA, Alonso-Díaz MÁ, Maza-Lopez J, Camas-Pereyra R, Olmedo-Juárez A, Higuera-Piedrahita RI, López-Arellano ME. Assembly and Analysis of Haemonchus contortus Transcriptome as a Tool for the Knowledge of Ivermectin Resistance Mechanisms. Pathogens 2023; 12:pathogens12030499. [PMID: 36986421 PMCID: PMC10059914 DOI: 10.3390/pathogens12030499] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Haemonchus contortus (Hc) is an important parasitic nematode of small ruminants. In this study we assembled the transcriptome of Hc as a model to contribute to the knowledge about the profile of the differential gene expression between two Mexican Hc strains under different anthelmintic resistance statuses, one susceptible and the other resistant to ivermectin (IVMs and IVMr, respectively), in order to improve and/or to have new strategies of control and diagnosis. The transcript sequence reads were assembled and annotated. Overall, ~127 Mbp were assembled and distributed into 77,422 transcript sequences, and 4394 transcripts of the de novo transcriptome were matched base on at least one of the following criteria: (1) Phylum Nemathelminthes and Platyhelminthes, important for animal health care, and (2) ≥55% of sequence identity with other organisms. The gene ontology (GO) enrichment analysis (GOEA) was performed to study the level of gene regulation to IVMr and IVMs strains using Log Fold Change (LFC) filtering values ≥ 1 and ≥ 2. The upregulated-displayed genes obtained via GOEA were: 1993 (for LFC ≥ 1) and 1241 (for LFC ≥ 2) in IVMr and 1929 (for LFC ≥ 1) and 835 (for LFC ≥ 2) in IVMs. The enriched GO terms upregulated per category identified the intracellular structure, intracellular membrane-bounded organelle and integral component of the cell membrane as some principal cellular components. Meanwhile, efflux transmembrane transporter activity, ABC-type xenobiotic transporter activity and ATPase-coupled transmembrane transporter activity were associated with molecular function. Responses to nematicide activity, pharyngeal pumping and positive regulation of synaptic assembly were classified as biological processes that might be involved in events related to the anthelmintic resistance (AR) and nematode biology. The filtering analysis of both LFC values showed similar genes related to AR. This study deepens our knowledge about the mechanisms behind the processes of H. contortus in order to help in tool production and to facilitate the reduction of AR and promote the development of other control strategies, such as anthelmintic drug targets and vaccines.
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Affiliation(s)
- David Emanuel Reyes-Guerrero
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Fed. Cuernavaca-Cuautla 8534, Jiutepec C.P. 62574, Morelos, Mexico
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico
| | - Verónica Jiménez-Jacinto
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico
| | - Rogelio Alejandro Alonso-Morales
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico
| | - Miguel Ángel Alonso-Díaz
- Centro de Enseñanza, Investigación y Extensión en Ganadería Tropical, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Km. 5. Carr. Fed. Tlapacoyan-Martínez de la Torre, Martínez de la Torre C.P. 93600, Veracruz, Mexico
| | - Jocelyn Maza-Lopez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Fed. Cuernavaca-Cuautla 8534, Jiutepec C.P. 62574, Morelos, Mexico
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico
| | - René Camas-Pereyra
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Fed. Cuernavaca-Cuautla 8534, Jiutepec C.P. 62574, Morelos, Mexico
| | - Agustín Olmedo-Juárez
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Fed. Cuernavaca-Cuautla 8534, Jiutepec C.P. 62574, Morelos, Mexico
| | - Rosa Isabel Higuera-Piedrahita
- Facultad de Estudios Superiores Cuautitlán, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Cuautitlán-Teoloyucan Km 2.5, Col. San Sebastián Xhala. Cuautitlán, C.P. 54714, Estado de México, Mexico
| | - María Eugenia López-Arellano
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carr. Fed. Cuernavaca-Cuautla 8534, Jiutepec C.P. 62574, Morelos, Mexico
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3
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Dimunová D, Matoušková P, Podlipná R, Boušová I, Skálová L. The role of UDP-glycosyltransferases in xenobiotic-resistance. Drug Metab Rev 2022; 54:282-298. [DOI: 10.1080/03602532.2022.2083632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Diana Dimunová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Petra Matoušková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Radka Podlipná
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Praha 6 - Lysolaje, Czech Republic
| | - Iva Boušová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lenka Skálová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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Salman M, Abbas RZ, Mehmood K, Hussain R, Shah S, Faheem M, Zaheer T, Abbas A, Morales B, Aneva I, Martínez JL. Assessment of Avermectins-Induced Toxicity in Animals. Pharmaceuticals (Basel) 2022; 15:332. [PMID: 35337129 PMCID: PMC8950826 DOI: 10.3390/ph15030332] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 01/02/2023] Open
Abstract
Macrocyclic lactones, particularly the avermectins, have completely revolutionized the approaches aimed at control of parasites. These avermectins are the most widely used anti-parasitic drugs in veterinary field with sales exceeding one billion US dollars annually. However, before clinical usage, their safety evaluation in the animals is a major critical factor that must be considered. Many studies have reported the negative effects of avermectins like ivermectin, abamectin, doramectin, and eprinomectin on the host animals. These harmful effects arise from avermectins targeting GABA and glutamate-gated chloride channels present both in the parasites and the host animals. In this review, various modes of avermectins action along with the negative effects on the host like nephrotoxicity, hepatotoxicity, neurotoxicity, reproductive toxicity, and endocrine disruption were discussed in detail. Furthermore, other important issues like ecotoxicity, drug resistance, and drug residues in milk associated with avermectins usage were also discussed, which need special attention.
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Affiliation(s)
- Muhammad Salman
- Department of Parasitology, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan; (M.S.); (S.S.); (T.Z.)
| | - Rao Zahid Abbas
- Department of Parasitology, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan; (M.S.); (S.S.); (T.Z.)
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Riaz Hussain
- Department of Pathology, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Sehar Shah
- Department of Parasitology, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan; (M.S.); (S.S.); (T.Z.)
| | - Mehwish Faheem
- Department of Zoology, Government College University Lahore, Lahore 54000, Pakistan;
| | - Tean Zaheer
- Department of Parasitology, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan; (M.S.); (S.S.); (T.Z.)
| | - Asghar Abbas
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan, Multan 59300, Pakistan;
| | - Bernardo Morales
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago de Chile, Estación Central, Santiago 9160000, Chile
| | - Ina Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - José L. Martínez
- Vicerrectoria de Investigación, Desarrollo e Innovación, Universidad de Santiago de Chile, Estación Central, Santiago 9160000, Chile
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5
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Gonzalez de la Rosa PM, Thomson M, Trivedi U, Tracey A, Tandonnet S, Blaxter M. A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. G3-GENES GENOMES GENETICS 2021; 11:6026964. [PMID: 33561231 PMCID: PMC8022731 DOI: 10.1093/g3journal/jkaa020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Eukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.
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Affiliation(s)
| | - Marian Thomson
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Sophie Tandonnet
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP 05508-090, Brazil
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
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6
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Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Commun Biol 2020; 3:656. [PMID: 33168940 PMCID: PMC7652881 DOI: 10.1038/s42003-020-01377-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/14/2020] [Indexed: 12/31/2022] Open
Abstract
Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite's life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Alan Tracey
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - David Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ, UK
| | - Wojtek Bazant
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Helen Beasley
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Robin Beech
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
| | - Karen Brooks
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
| | - Axel Martinelli
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jennifer D Noonan
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Michael A Quail
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Faye H Rodgers
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Guillaume Sallé
- INRAE - U. Tours, UMR 1282 ISP Infectiologie et Santé Publique, Centre de recherche Val de Loire, Nouzilly, France
| | | | | | - Janneke Wit
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - James A Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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Ma G, Gasser RB, Wang T, Korhonen PK, Young ND. Toward integrative 'omics of the barber's pole worm and related parasitic nematodes. INFECTION GENETICS AND EVOLUTION 2020; 85:104500. [PMID: 32795511 DOI: 10.1016/j.meegid.2020.104500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid sequencing, mass spectrometry and computational biology have facilitated the identification, annotation and analysis of genes, transcripts, proteins and metabolites in model nematodes (Caenorhabditis elegans and Pristionchus pacificus) and socioeconomically important parasitic nematodes (Clades I, III, IV and V). Significant progress has been made in genomics and transcriptomics as well as in the proteomics and lipidomics of Haemonchus contortus (the barber's pole worm) - one of the most pathogenic representatives of the order Strongylida. Here, we review salient aspects of genomics, transcriptomics, proteomics, lipidomics, glycomics and functional genomics, and discuss the rise of integrative 'omics of this economically important parasite. Although our knowledge of the molecular biology, genetics and biochemistry of H. contortus and related species has progressed significantly, much remains to be explored, particularly in areas such as drug resistance, unique/unknown genes, host-parasite interactions, parasitism and the pathogenesis of disease, by integrating the use of multiple 'omics methods. This approach should lead to a better understanding of H. contortus and its relatives at a 'systems biology' level, and should assist in developing new interventions against these parasites.
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Affiliation(s)
- Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China; Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
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Elucidating the molecular and developmental biology of parasitic nematodes: Moving to a multiomics paradigm. ADVANCES IN PARASITOLOGY 2020; 108:175-229. [PMID: 32291085 DOI: 10.1016/bs.apar.2019.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the past two decades, significant progress has been made in the sequencing, assembly, annotation and analyses of genomes and transcriptomes of parasitic worms of socioeconomic importance. This progress has somewhat improved our knowledge and understanding of these pathogens at the molecular level. However, compared with the free-living nematode Caenorhabditis elegans, the areas of functional genomics, transcriptomics, proteomics and metabolomics of parasitic nematodes are still in their infancy, and there are major gaps in our knowledge and understanding of the molecular biology of parasitic nematodes. The information on signalling molecules, molecular pathways and microRNAs (miRNAs) that are known to be involved in developmental processes in C. elegans and the availability of some molecular resources (draft genomes, transcriptomes and some proteomes) for selected parasitic nematodes provide a basis to start exploring the developmental biology of parasitic nematodes. Indeed, some studies have identified molecules and pathways that might associate with developmental processes in related, parasitic nematodes, such as Haemonchus contortus (barber's pole worm). However, detailed information is often scant and 'omics resources are limited, preventing a proper integration of 'omic data sets and comprehensive analyses. Moreover, little is known about the functional roles of pheromones, hormones, signalling pathways and post-transcriptional/post-translational regulations in the development of key parasitic nematodes throughout their entire life cycles. Although C. elegans is an excellent model to assist molecular studies of parasitic nematodes, its use is limited when it comes to explorations of processes that are specific to parasitism within host animals. A deep understanding of parasitic nematodes, such as H. contortus, requires substantially enhanced resources and the use of integrative 'omics approaches for analyses. The improved genome and well-established in vitro larval culture system for H. contortus provide unprecedented opportunities for comprehensive studies of the transcriptomes (mRNA and miRNA), proteomes (somatic, excretory/secretory and phosphorylated proteins) and lipidomes (e.g., polar and neutral lipids) of this nematode. Such resources should enable in-depth explorations of its developmental biology at a level, not previously possible. The main aims of this review are (i) to provide a background on the development of nematodes, with a particular emphasis on the molecular aspects involved in the dauer formation and exit in C. elegans; (ii) to critically appraise the current state of knowledge of the developmental biology of parasitic nematodes and identify key knowledge gaps; (iii) to cover salient aspects of H. contortus, with a focus on the recent advances in genomics, transcriptomics, proteomics and lipidomics as well as in vitro culturing systems; (iv) to review recent advances in our knowledge and understanding of the molecular and developmental biology of H. contortus using an integrative multiomics approach, and discuss the implications of this approach for detailed explorations of signalling molecules, molecular processes and pathways likely associated with nematode development, adaptation and parasitism, and for the identification of novel intervention targets against these pathogens. Clearly, the multiomics approach established recently is readily applicable to exploring a wide range of interesting and socioeconomically significant parasitic worms (including also trematodes and cestodes) at the molecular level, and to elucidate host-parasite interactions and disease processes.
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Jasmer DP, Rosa BA, Tyagi R, Mitreva M. Omics Driven Understanding of the Intestines of Parasitic Nematodes. Front Genet 2019; 10:652. [PMID: 31402928 PMCID: PMC6669237 DOI: 10.3389/fgene.2019.00652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/19/2019] [Indexed: 01/25/2023] Open
Abstract
The biological and molecular complexity of nematodes has impeded research on development of new therapies for treatment and control. We have focused on the versatility of the nematode intestine as a target for new therapies. To that end, it is desirable to establish a broad and deep understanding of the molecular architecture underlying intestinal cell functions at the pan-Nematoda level. Multiomics data were generated to uncover the evolutionary principles underlying both conserved and adaptable features of the nematode intestine. Whole genomes were used to reveal the functional potential of the nematodes, tissue-specific transcriptomes provided a deep assessment of genes that are expressed in the adult nematode intestine, and comparison of selected core species was used to determine a first approximation of the pan-Nematoda intestinal transcriptome. Differentially expressed transcripts were also identified among intestinal regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. Profiling intestinal miRNAs targeting these genes identified the conserved intestinal miRNAs. Proteomics of intestinal cell compartments assigned proteins to several different intestinal cell compartments (intestinal tissue, the integral and peripheral intestinal membranes, and the intestinal lumen). Finally, advanced bioinformatic approaches were used to predict intestinal cell functional categories of seminal importance to parasite survival, which can now be experimentally tested and validated. The data provide the most comprehensive compilation of constitutively and differentially expressed genes, predicted gene regulators, and proteins of the nematode intestine. The information provides knowledge that is essential to understand molecular features of nematode intestinal cells and functions of fundamental importance to the intestine of many, if not all, parasitic nematodes.
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Affiliation(s)
- Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Rahul Tyagi
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University, St. Louis, St. Louis, MI, United States.,Department of Internal Medicine, Washington University School of Medicine, St. Louis, MI, United States
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Ma G, Wang T, Korhonen PK, Stroehlein AJ, Young ND, Gasser RB. Dauer signalling pathway model for Haemonchus contortus. Parasit Vectors 2019; 12:187. [PMID: 31036054 PMCID: PMC6489264 DOI: 10.1186/s13071-019-3419-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/28/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Signalling pathways have been extensively investigated in the free-living nematode Caenorhabditis elegans, but very little is known about these pathways in parasitic nematodes. Here, we constructed a model for the dauer-associated signalling pathways in an economically highly significant parasitic worm, Haemonchus contortus. METHODS Guided by data and information available for C. elegans, we used extensive genomic and transcriptomic datasets to infer gene homologues in the dauer-associated pathways, explore developmental transcriptomic, proteomic and phosphoproteomic profiles in H. contortus and study selected molecular structures. RESULTS The canonical cyclic guanosine monophosphate (cGMP), transforming growth factor-β (TGF-β), insulin-like growth factor 1 (IGF-1) and steroid hormone signalling pathways of H. contortus were inferred to represent a total of 61 gene homologues. Compared with C. elegans, H. contortus has a reduced set of genes encoding insulin-like peptides, implying evolutionary and biological divergences between the parasitic and free-living nematodes. Similar transcription profiles were found for all gene homologues between the infective stage of H. contortus and dauer stage of C. elegans. High transcriptional levels for genes encoding G protein-coupled receptors (GPCRs), TGF-β, insulin-like ligands (e.g. ins-1, ins-17 and ins-18) and transcriptional factors (e.g. daf-16) in the infective L3 stage of H. contortus were suggestive of critical functional roles in this stage. Conspicuous protein expression patterns and extensive phosphorylation of some components of these pathways suggested marked post-translational modifications also in the L3 stage. The high structural similarity in the DAF-12 ligand binding domain among nematodes indicated functional conservation in steroid (i.e. dafachronic acid) signalling linked to worm development. CONCLUSIONS Taken together, this pathway model provides a basis to explore hypotheses regarding biological processes and regulatory mechanisms (via particular microRNAs, phosphorylation events and/or lipids) associated with the development of H. contortus and related nematodes as well as parasite-host cross talk, which could aid the discovery of new therapeutic targets.
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Affiliation(s)
- Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Andreas J. Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
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11
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Mating barriers between genetically divergent strains of the parasitic nematode Haemonchus contortus suggest incipient speciation. Int J Parasitol 2019; 49:531-540. [PMID: 31034791 DOI: 10.1016/j.ijpara.2019.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/25/2019] [Accepted: 02/03/2019] [Indexed: 11/21/2022]
Abstract
Haemonchus contortus, in common with many nematode species, has extremely high levels of genetic variation within and between field populations derived from distant geographical locations. MHco10(CAVR), MHco3(ISE) and MHco4(WRS) are genetically divergent H. contortus strains, originally derived from Australia, Kenya and South Africa, respectively, that have been maintained by numerous rounds of in vivo experimental infection of sheep. In order to explore potential pre-zygotic competition or post-zygotic incompatibility between the strains, we have investigated the ability of MHco10(CAVR) to interbreed with either MHco3(ISE) or MHco4(WRS) during dual strain co-infections. Sheep were experimentally co-infected with 4000 infective larvae (L3) per os of the MHco10(CAVR) strain and an equal number of either the MHco3(ISE) or the MHco4(WRS) strain L3. The adult worm establishement rates and the proportions of F1 progeny resulting from intra- and inter-strain mating events were determined by admixture analysis of microsatellite multi-locus genotypes. Although there was no difference in adult worm establishment rates, the proportions of F1 progeny of both the MHco10(CAVR) × MHco3(ISE) and MHco10(CAVR) × MHco4(WRS) dual strain co-infections departed from Mendelian expectations. The proportions of inter-strain hybrid F1 progeny were lower than the expected 50%, suggesting either pre-zygotic competition or post-zygotic incompatibility between the co-infecting strains. To investigate this further, both eggs and hatched L1 of broods from single adult female worms recovered from each dual co-infection were genotyped. Unhatched eggs from the broods revealed no inter-strain hybrid genotype deficit, suggesting there is no pre-zygotic competition between the strains. In contrast, there was a deficit in L1 inter-strain hybrid genotypes in the broods derived from MHco3(ISE) or MHco4(WRS) maternal parents, but not from MHco10(CAVR) maternal parents. This suggests that hybrid progeny of MHco10(CAVR) paternal parents have reduced post-zygotic development and/or viability consistent with incipient speciation of the MHco10(CAVR) strain. The presence of mating barriers between allopatric H. contortus strains has important implications for parasite ecology, including the ability of newly introduced anthelmintic-resistant parasite populations to compete and interbreed with populations already established in a region.
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12
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Doyle SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA, Tait A, Tracey A, Berriman M, Devaney E, Cotton JA, Sargison ND. A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry. Genome Biol Evol 2018; 10:396-409. [PMID: 29267942 PMCID: PMC5793844 DOI: 10.1093/gbe/evx269] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/27/2022] Open
Abstract
The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - David J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Barbara K Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
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13
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A method for single pair mating in an obligate parasitic nematode. Int J Parasitol 2017; 48:159-165. [PMID: 29111440 DOI: 10.1016/j.ijpara.2017.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 11/23/2022]
Abstract
Parasitic nematode species have extremely high levels of genetic diversity, presenting a number of experimental challenges for genomic and genetic work. Consequently, there is a need to develop inbred laboratory strains with reduced levels of polymorphism. The most efficient approach to inbred line development is single pair mating, but this is challenging for obligate parasites where the adult sexual reproductive stages are inside the host, and thus difficult to experimentally manipulate. This paper describes a successful approach to single pair mating of a parasitic nematode, Haemonchus contortus. The method allows for polyandrous mating behaviour and involves the surgical transplantation of a single adult male worm with multiple immature adult females directly into the sheep abomasum. We used a panel of microsatellite markers to monitor and validate the single pair mating crosses and to ensure that the genotypes of progeny and subsequent filial generations were consistent with those expected from a mating between a single female parent of known genotype and a single male parent of unknown genotype. We have established two inbred lines that both show a significant overall reduction in genetic diversity based on microsatellite genotyping and genome-wide single nucleotide polymorphism. There was an approximately 50% reduction in heterozygous SNP sites across the genome in the MHco3.N1 line compared with the MoHco3(ISE) parental strain. The MHco3.N1 inbred line has subsequently been used to provide DNA template for whole genome sequencing of H. contortus. This work provides proof of concept and methodologies for forward genetic analysis of obligate parasitic nematodes.
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Wit J, Gilleard JS. Resequencing Helminth Genomes for Population and Genetic Studies. Trends Parasitol 2017; 33:388-399. [DOI: 10.1016/j.pt.2017.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
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Laing R, Gillan V, Devaney E. Ivermectin - Old Drug, New Tricks? Trends Parasitol 2017; 33:463-472. [PMID: 28285851 PMCID: PMC5446326 DOI: 10.1016/j.pt.2017.02.004] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 11/30/2022]
Abstract
Ivermectin is one of the most important drugs in veterinary and human medicine for the control of parasitic infection and was the joint focus of the 2015 Nobel Prize in Physiology or Medicine, some 35 years after its remarkable discovery. Although best described for its activity on glutamate-gated chloride channels in parasitic nematodes, understanding of its mode of action remains incomplete. In the field of veterinary medicine, resistance to ivermectin is now widespread, but the mechanisms underlying resistance are unresolved. Here we discuss the history of this versatile drug and its use in global health. Based on recent studies in a variety of systems, we question whether ivermectin could have additional modes of action on parasitic nematodes. Ligand-gated ion channels, particularly glutamate-gated chloride channels, are well characterised as the targets of IVM in nematodes and insects. Nematode genomes are helping to cast light on the diversity of ion-channel subunits in different parasite species of human and veterinary importance. Resistance to IVM is an increasing problem in the control of parasitic nematodes, and resolving the mechanisms is an important research priority. Recent studies in other biological systems suggest that IVM can affect a number of additional pathways. IVM may have novel applications in the treatment and control of important human diseases.
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Affiliation(s)
- Roz Laing
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK.
| | - Victoria Gillan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - Eileen Devaney
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
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Emery DL, Hunt PW, Le Jambre LF. Haemonchus contortus: the then and now, and where to from here? Int J Parasitol 2016; 46:755-769. [DOI: 10.1016/j.ijpara.2016.07.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/16/2022]
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