Melbourne Veterinary School - Research Publications

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    Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
    Ma, G ; Wang, T ; Korhonen, PK ; Young, ND ; Nie, S ; Ang, C-S ; Williamson, NA ; Reid, GE ; Gasser, RB ; Streit, A (PUBLIC LIBRARY SCIENCE, 2019-07-01)
    Here, we discovered an endogenous dafachronic acid (DA) in the socioeconomically important parasitic nematode Haemonchus contortus. We demonstrate that DA promotes larval exsheathment and development in this nematode via a relatively conserved nuclear hormone receptor (DAF-12). This stimulatory effect is dose- and time-dependent, and relates to a modulation of dauer-like signalling, and glycerolipid and glycerophospholipid metabolism, likely via a negative feedback loop. Specific chemical inhibition of DAF-9 (cytochrome P450) was shown to significantly reduce the amount of endogenous DA in H. contortus; compromise both larval exsheathment and development in vitro; and modulate lipid metabolism. Taken together, this evidence shows that DA plays a key functional role in the developmental transition from the free-living to the parasitic stage of H. contortus by modulating the dauer-like signalling pathway and lipid metabolism. Understanding the intricacies of the DA-DAF-12 system and associated networks in H. contortus and related parasitic nematodes could pave the way to new, nematode-specific treatments.
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    Gene content evolution in the arthropods
    Thomas, GWC ; Dohmen, E ; Hughes, DST ; Murali, SC ; Poelchau, M ; Glastad, K ; Anstead, CA ; Ayoub, NA ; Batterham, P ; Bellair, M ; Binford, GJ ; Chao, H ; Chen, YH ; Childers, C ; Dinh, H ; Doddapaneni, HV ; Duan, JJ ; Dugan, S ; Esposito, LA ; Friedrich, M ; Garb, J ; Gasser, RB ; Goodisman, MAD ; Gundersen-Rindal, DE ; Han, Y ; Handler, AM ; Hatakeyama, M ; Hering, L ; Hunter, WB ; Ioannidis, P ; Jayaseelan, JC ; Kalra, D ; Khila, A ; Korhonen, PK ; Lee, CE ; Lee, SL ; Li, Y ; Lindsey, ARI ; Mayer, G ; McGregor, AP ; McKenna, DD ; Misof, B ; Munidasa, M ; Munoz-Torres, M ; Muzny, DM ; Niehuis, O ; Osuji-Lacy, N ; Palli, SR ; Panfilio, KA ; Pechmann, M ; Perry, T ; Peters, RS ; Poynton, HC ; Prpic, N-M ; Qu, J ; Rotenberg, D ; Schal, C ; Schoville, SD ; Scully, ED ; Skinner, E ; Sloan, DB ; Stouthamer, R ; Strand, MR ; Szucsich, NU ; Wijeratne, A ; Young, ND ; Zattara, EE ; Benoit, JB ; Zdobnov, EM ; Pfrender, ME ; Hackett, KJ ; Werren, JH ; Worley, KC ; Gibbs, RA ; Chipman, AD ; Waterhouse, RM ; Bornberg-Bauer, E ; Hahn, MW ; Richards, S (BMC, 2020-01-23)
    BACKGROUND: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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    Dauer signalling pathway model for Haemonchus contortus
    Ma, G ; Wang, T ; Korhonen, PK ; Stroehlein, AJ ; Young, ND ; Gasser, RB (BMC, 2019-04-29)
    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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    Long-read sequencing reveals a 4.4kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1
    Kinkar, L ; Korhonen, PK ; Cai, H ; Gauci, CG ; Lightowlers, MW ; Saarma, U ; Jenkins, DJ ; Li, J ; Li, J ; Young, ND ; Gasser, RB (BMC, 2019-05-16)
    BACKGROUND: Echinococcus tapeworms cause a severe helminthic zoonosis called echinococcosis. The genus comprises various species and genotypes, of which E. granulosus (sensu stricto) represents a significant global public health and socioeconomic burden. Mitochondrial (mt) genomes have provided useful genetic markers to explore the nature and extent of genetic diversity within Echinococcus and have underpinned phylogenetic and population structure analyses of this genus. Our recent work indicated a sequence gap (> 1 kb) in the mt genomes of E. granulosus genotype G1, which could not be determined by PCR-based Sanger sequencing. The aim of the present study was to define the complete mt genome, irrespective of structural complexities, using a long-read sequencing method. METHODS: We extracted high molecular weight genomic DNA from protoscoleces from a single cyst of E. granulosus genotype G1 from a sheep from Australia using a conventional method and sequenced it using PacBio Sequel (long-read) technology, complemented by BGISEQ-500 short-read sequencing. Sequence data obtained were assembled using a recently-developed workflow. RESULTS: We assembled a complete mt genome sequence of 17,675 bp, which is > 4 kb larger than the complete mt genomes known for E. granulosus genotype G1. This assembly includes a previously-elusive tandem repeat region, which is 4417 bp long and consists of ten near-identical 441-445 bp repeat units, each harbouring a 184 bp non-coding region and adjacent regions. We also identified a short non-coding region of 183 bp, which includes an inverted repeat. CONCLUSIONS: We report what we consider to be the first complete mt genome of E. granulosus genotype G1 and characterise all repeat regions in this genome. The numbers, sizes, sequences and functions of tandem repeat regions remain to be studied in different isolates of genotype G1 and in other genotypes and species. The discovery of such 'new' repeat elements in the mt genome of genotype G1 by PacBio sequencing raises a question about the completeness of some published genomes of taeniid cestodes assembled from conventional or short-read sequence datasets. This study shows that long-read sequencing readily overcomes the challenges of assembling repeat elements to achieve improved genomes.
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    Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions
    Anstead, CA ; Korhonen, PK ; Young, ND ; Hall, RS ; Jex, AR ; Murali, SC ; Hughes, DST ; Lee, SF ; Perry, T ; Stroehlein, AJ ; Ansell, BRE ; Breugelmans, B ; Hofmann, A ; Qu, J ; Dugan, S ; Lee, SL ; Chao, H ; Dinh, H ; Han, Y ; Doddapaneni, HV ; Worley, KC ; Muzny, DM ; Ioannidis, P ; Waterhouse, RM ; Zdobnov, EM ; James, PJ ; Bagnall, NH ; Kotze, AC ; Gibbs, RA ; Richards, S ; Batterham, P ; Gasser, RB (NATURE PUBLISHING GROUP, 2015-06-01)
    Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
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    Use of a bioinformatic-assisted primer design strategy to establish a new nested PCR-based method for Cryptosporidium
    Koehler, AV ; Korhonen, PK ; Hall, RS ; Young, ND ; Wang, T ; Haydon, SR ; Gasser, RB (BMC, 2017-10-23)
    BACKGROUND: The accurate tracking of Cryptosporidium in faecal, water and/or soil samples in water catchment areas is central to developing strategies to manage the potential risk of cryptosporidiosis transmission to humans. Various PCR assays are used for this purpose. Although some assays achieve specific amplification from Cryptosporidium DNA in animal faecal samples, some do not. Indeed, we have observed non-specificity of some oligonucleotide primers in the small subunit of nuclear ribosomal RNA gene (SSU), which has presented an obstacle to the identification and classification of Cryptosporidium species and genotypes (taxa) from faecal samples. RESULTS: Using a novel bioinformatic approach, we explored all available Cryptosporidium genome sequences for new and diagnostically-informative, multi-copy regions to specifically design oligonucleotide primers in the large subunit of nuclear ribosomal RNA gene (LSU) as a basis for an effective nested PCR-based sequencing method for the identification and/or classification of Cryptosporidium taxa. CONCLUSION: This newly established PCR, which has high analytical specificity and sensitivity, is now in routine use in our laboratory, together with other assays developed by various colleagues. Although the present bioinformatic workflow used here was for the specific design of primers in nuclear DNA of Cryptosporidium, this approach should be broadly applicable to many other microorganisms.