Research paperToward integrative ‘omics of the barber’s pole worm and related parasitic nematodes
Introduction
In the 1920s, the term “genome” was used to define the complete set of genes of an organism (Kuska, 1998). Since then, the suffix “ome” has been widely used to represent molecular components (e.g., transcripts, proteins and metabolites) within a cell, tissue or organism, such as the transcriptome, proteome and metabolome, with the suffix “omics” referring to the related technical and research aspects (Lederberg and Mccray, 2001; Prohaska and Stadler, 2011; Swinbanks, 1995; Yadav, 2007).
A number of review articles (Aebersold and Mann, 2016; Cantacessi et al., 2012; Domon and Aebersold, 2006; Metzker, 2010; Wang et al., 2009) describe how major technological developments in nucleic acid sequencing, mass spectrometry and bioinformatics have contributed to the rise of the ‘omics field, significantly accelerating biological explorations of organisms at the molecular level. For instance, decoding the genome of Caenorhabditis elegans (C. elegans Sequencing Consortium, 1998) marked a milestone for biological investigations of metazoans, initiating extensive genomics, transcriptomics, proteomics, glycomics, lipidomics and metabolomics of this free-living model nematode to achieve a comprehensive molecular understanding (Corsi et al., 2015; Girard et al., 2007; Van Assche et al., 2015; Watts and Ristow, 2017). Nonetheless, in comparison, much less has been achieved for parasitic nematodes, particularly for those of veterinary significance (International Helminth Genomes Consortium, 2019; Jex et al., 2019) (Fig. 1).
Nematodes within the order Strongylida are the largest group of worms of animals and include species of Haemonchus, Trichostrongylus, Ostertagia, Teladorsagia, Cooperia, Nematodirus, Oesophagostomum and Chabertia (Chilton et al., 2006). One of the most pathogenic representatives of this group (order) is the haematophagous nematode Haemonchus contortus. It lives in the abomasa of sheep, goats and other ruminants, causing haemonchosis, characterised by anaemia, oedema and associated complications, and affecting hundreds of millions of livestock animals globally (Gasser and von Samson-Himmelstjerna, 2016). The control of haemonchosis relies heavily on anthelmintic treatment (e.g., moxidectin and monepantel), in spite of a commercial vaccine being available for use in lambs (Besier et al., 2016; McKellar and Jackson, 2004). However, due to the excessive use of anthelmintics, drug resistance has become a major challenge for the control of nematodes, particularly in H. contortus and other strongylids of veterinary significance (Geerts and Gryseels, 2001; Kaplan, 2004; Playford et al., 2014; Sutherland and Leathwick, 2011; Wolstenholme et al., 2004). Revealing the mechanisms of drug resistance and discovering novel targets for drugs or vaccines are key priorities in nematode research, and should be based on a deep understanding of H. contortus and other parasitic nematodes at the molecular level.
The life cycle of H. contortus consists of a free-living phase in the environment and a parasitic phase in the host animal: embryonated eggs are excreted into the environment via host faeces; first-stage larvae (L1) hatch within 1 day, develop and moult to become second-stage (L2) and then third-stage larvae (L3) within 7 days; the L3 stage, after it undergoes developmental arrest, can persist on pasture for weeks or months; following ingestion by the host animal, infective L3s exsheath, moult and develop to become fourth-stage larvae (L4) and then dioecious (female and male) adults ~11 days after ingestion. Both L4s and adults feed on blood from capillaries in the abomasal wall, and female adult worms produce fertilised eggs ~21 days after infection (Veglia, 1915). The direct and short life cycle as well as the high reproductive potential of H. contortus make this nematode relatively easy to maintain in experimental animals and to be a useful model for biological explorations. In particular, due to its high propensity to develop resistance to anthelmintics (Gilleard, 2013; Prichard, 2001), and its close phylogenetic relationship to the model organism C. elegans, H. contortus has become a representative nematode in the research fields of drug resistance (Gillan et al., 2017; Gilleard, 2013; Lanusse et al., 2016), drug discovery (Geary, 2016; Jiao et al., 2020; Preston et al., 2016) and vaccine development (Besier et al., 2012, Besier et al., 2015; Laing et al., 2013).
Supporting these areas have been advances in the genomics, transcriptomics, proteomics and lipidomics of H. contortus, elevating this worm to the most studied parasitic nematode of the order Strongylida at the molecular level (Fig. 1). In particular, over the past 20 years, the discovery and characterisation of individual genes, mRNAs, non-coding RNAs and proteins have been followed by high-throughput, quantitative profiling of these molecules, providing unprecedented insights into the molecular biology of H. contortus and starting a new era of genomics and integrative ‘omics of this important parasite (Fig. 2). In this article, we review salient aspects of the genomics, transcriptomics, proteomics, lipidomics and glycomics of H. contortus, discuss the rising trend toward integrative ‘omics, and propose complementary research areas (e.g., metabolomics and genome-wide functional genomics) to achieve a better understanding of this and related socioeconomically important parasitic nematodes.
Section snippets
Genomes and population genomics of H. contortus
Using long-PCR based 454 sequencing technology, the mitochondrial genome of H. contortus (McMaster strain) was reported more than 10 years ago (Jex et al., 2008). This mitochondrial genome was reported to be 14,055 bp in length and highly AT-rich (78.1%), containing 12 protein-coding genes (atp6, cox1–3, cytb, nad1–6 and nad4L), 22 trn genes, a rrnL gene and a rrnS gene (Jex et al., 2008). Recently, two more complete mitochondrial genomes were reported for a MHco3(ISE) strain and a New Zealand
Transcriptomes and transcriptomic analyses of H. contortus
Sequencing expressed sequence tags (EST) provided valuable information on the transcription of mRNAs in H. contortus (Cantacessi et al., 2010; Hoekstra et al., 2000; Yin et al., 2008). However, the EST-based approach was labour intensive and time consuming; particularly quantitative analysis of EST-based data required additional work, such as microarrays (Campbell et al., 2008), hindering high-throughput exploration of H. contortus at the molecular level.
The development of RNA-seq technology
Somatic, excretory/secretory and phosphorylated proteomics of H. contortus
The availability of genome and transcriptome datasets have been used to infer a proteome for H. contortus, consisting of >20,000 proteins (Doyle et al., 2018; Laing et al., 2013; Palevich et al., 2019; Schwarz et al., 2013). However, only 4036 actual protein sequences have been deposited in the UniProt database (https://www.uniprot.org), with most of them needing review, and only 19 having genuine annotation. It is expected that this issue will be resolved following the deposition of the new
Lipidomes and lipidomic explorations of H. contortus
The roles of lipid metabolism (e.g., involving fatty acids and steroid hormones) in development, reproduction, adaptation and parasitism and drug resistance have been indicated in previous molecular studies of H. contortus (Campbell et al., 2008; Laing et al., 2015; Li et al., 2014; Ma et al., 2018; Wang et al., 2019a). However, proposals about lipids and their functions in H. contortus rely mainly on knowledge from C. elegans (Harder, 2016; Watts and Ristow, 2017; Witting and Schmitt-Kopplin,
Functional genomics of H. contortus
Compared with the significant progress achieved in the genomics, transcriptomics, proteomics and lipidomics of H. contortus, advances in functional genomics of this and related nematodes have been modest. The paucity of functional information for most molecules relates to a lack of effective functional genomic platforms and difficulties associated with maintaining the complete lifecycle of H. contortus and other strongylids in the laboratory. Nonetheless, there have been some important
Exploring the developmental biology of H. contortus by integrating ‘omic data sets
Recent advances in genomics, transcriptomics, proteomics and lipidomics as well as functional genomics of H. contortus have identified a landscape of genes, transcripts, proteins and lipids as well as functional information for this parasitic nematode (Fig. 2). In particular, analyses of individual genome, transcriptome, proteome and lipidome data sets have discovered some interesting biological aspects of development and reproduction, adaptation and parasitism and/or drug resistance of H.
Concluding remarks
In the past 20 years, major advances have been made in the genomics, transcriptomics, proteomics, lipidomics and functional genomics of H. contortus, providing unprecedented opportunities to gain a better understanding of this economically important parasitic nematode at the molecular level. In particular, the availability of chromosome-contiguous reference genomes has allowed comprehensive population genomic investigations, and will clearly be beneficial to a wide range of genetic, biological
Acknowledgements
Funding from the Australian Research Council (ARC), National Health and Medical Research Council (NHMRC) of Australia, BGI International Pty Ltd and Yourgene Health, Melbourne Water is gratefully acknowledged. N.D.Y. held an NHMRC Career Development Fellowship, and P.K.K. holds an NHMRC Early Career Research Fellowship. Project support was through ARC grants LP180101334 (N.D.Y. and P.K.K.) and LP180101085 (R.B.G.).
Declaration of Competing Interest
None of the authors has a conflict interest.
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2022, Biotechnology AdvancesCitation Excerpt :Although not routinely applied to parasitic worms in the academic context, use of such high-content platforms would substantially accelerate and enhance the accuracy of high-throughput screening for early phase anthelmintic discovery. Based on recent published evidence, it is anticipated that integrative ‘omic, chemoinformatic and/or advanced bioinformatics (e.g., machine and deep learning) approaches (Lo et al., 2018; Ma et al., 2020; Elbadawi et al., 2021) will enable the prediction and prioritisation of drug targets (Campos et al., 2020a, 2020b), annotation and structural modelling of such targets (Alphafold; Jumper et al., 2021; Varadi et al., 2021), the selection of small molecule candidates (Agamah et al., 2020) and molecular simulation of binding of small molecules to predicted targets (Bagherian et al., 2021) in silico prior to detailed laboratory experimentation. Such in silico, biology-guided approaches, once validated, might be able to guide the selection of chemical entities/groups to be screened on particular parasite species and/or targets, with the potential of increasing efficiency, reducing costs and accelerating the drug discovery/development process overall.
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2021, Current Research in Parasitology and Vector-Borne DiseasesCitation Excerpt :Over the past two decades, substantial progress has been made in the field of molecular parasitology using genomic, transcriptomic and proteomic technologies (International Helminth Genomes, 2019; Jex et al., 2019; Ma et al., 2020b; McVeigh, 2020). Numerous studies of parasitic worms have focused on the identification and characterisation of genes and proteins (Ma et al., 2020a; McVeigh, 2020). Some of these studies have identified and/or annotated a large number of genes and proteins which are associated with the biosynthesis and transportation of lipids (e.g. International Helminth Genomes, 2019), and significant changes in transcription/expression profiles in the transition from free-living to parastitic stages (Laing et al., 2013; Wang et al., 2019b).