One species, two genomes: A critical assessment of inter-isolate variation and identification of assembly incongruence in Haemonchus contortus

AbstractBackgroundNumerous quality issues may compromise genomic data’s representation of its underlying organism. In this study, we compared two genomes published by different research groups for the parasitic nematode Haemonchus contortus, corresponding to divergent isolates. We analyzed differences between the genomes, attempting to ascertain which were attributable to legitimate biological differences, and which to technical error in one or both genomes.ResultsWe found discrepancies between the H. contortus genomes in both assembly and annotation. The genomes differed in representation of genes that are highly conserved across eukaryotes, with clear evidence of misassembly underlying conserved genes missing from one genome or the other. Only 45% of genes in one genome were orthologous to genes in the other genome, with one genome exhibiting almost as much orthology to C. elegans as its counterpart H. contortus strain. The two genomes differed substantially in probable causes underlying this unexpectedly low orthology. One genome included many more inparalogues than the other, and more frequently assembled inparalogues together on the same portions of contiguous sequence. It also exhibited cases of better-conserved gene position relative to C. elegans.ConclusionThe discrepancies between the two genomes far exceeded those expected as a consequence of biological differences between the two H. contortus isolates. This implies substantial quality issues in one or both genomes, suggesting that researchers must exercise caution when using genomic data for newly sequenced species.

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Complementary Approaches to Understand Anthelmintic Resistance Using Free-Living and Parasitic Nematodes

10.20944/preprints202008.0313.v2 ◽

2020 ◽

Author(s):

Janneke Wit ◽

Clayton Dilks ◽

Erik Andersen

Keyword(s):

Haemonchus Contortus ◽

Parasitic Nematode ◽

Anthelmintic Resistance ◽

Nematode Species ◽

The Other ◽

Parasitic Nematodes ◽

Mechanisms Of Resistance ◽

Free Living ◽

Sustained Efficacy ◽

Modes Of Action

Anthelmintic drugs are the major line of defense against parasitic nematode infections, but the arsenal is limited and resistance threatens sustained efficacy of the available drugs. Discoveries of the modes of action of these drugs and mechanisms of resistance have predominantly come from studies of a related non-parasitic nematode species, Caenorhabditis elegans, and the parasitic nematode Haemonchus contortus. Here, we discuss how our understanding of anthelmintic resistance and modes of action came from the interplay of results from each of these species. We argue that this “cycle of discovery”, where results from one species inform the design of experiments in the other, can use the complementary strengths of both to understand anthelmintic modes of action and mechanisms of resistance.

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In vitro demonstration of in utero larval development in an oviparous parasitic nematode: Haemonchus contortus

Parasitology ◽

10.1017/s0031182000051532 ◽

1986 ◽

Vol 93 (2) ◽

pp. 371-381

Author(s):

Liyew Ayalew ◽

Beverley E. Pearson Murphy

Keyword(s):

Haemonchus Contortus ◽

Parasitic Nematode ◽

Normal Development ◽

Gravid Female ◽

Current Control ◽

Control Measures ◽

The Other ◽

Epidemiological Features

SUMMARYThe life-cycle of Haemonchus contortus, a pathogenic stomach nematode of sheep, is typical of those of the other members of the superfamily Trichostrongyloides, all of which require a period of development outside the definitive host. Classically, gravid H. contortus, known as strictly oviparous, releases her eggs into the abomasal lumen. The eggs are passed out in the faeces in which they hatch into the 1st-stage larvae and then develop into the infective 3rd-stage larvae. We have developed a method to study the fate of eggs within gravid worms. Using this procedure, we have shown that H. contortus may also exhibit viviparity with apparently normal development from the egg to the 4th larval stage taking place within the gravid female maintained in vitro. On the basis of these observations we speculate that viviparity might occur in vivo with consequent autoinfections; if so, this might explain some puzzling clinical and epidemiological features of haemonchosis, as well as the incomplete efficacy of current control measures.

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Two novel loci underlie natural differences in Caenorhabditis elegans macrocyclic lactone responses

10.1101/2021.01.14.426644 ◽

2021 ◽

Author(s):

Kathryn S. Evans ◽

Janneke Wit ◽

Lewis Stevens ◽

Steffen R. Hahnel ◽

Briana Rodriguez ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Haemonchus Contortus ◽

Macrocyclic Lactone ◽

Parasitic Nematode ◽

Anthelmintic Resistance ◽

Recombinant Inbred Lines ◽

Parasitic Nematodes ◽

C Elegans ◽

The Future ◽

Genomic Regions

AbstractParasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.Author SummaryParasitic nematodes infect plants, animals, and humans, causing major health and economic burdens worldwide. Parasitic nematode infections are generally treated efficiently with a class of drugs named anthelmintics. However, resistance to many of these anthelmintic drugs, including macrocyclic lactones (MLs), is rampant and increasing. Therefore, it is essential that we understand how these drugs act against parasitic nematodes and, conversely, how nematodes gain resistance in order to better treat these infections in the future. Here, we used the non-parasitic nematode Caenorhabditis elegans as a model organism to study ML resistance. We leveraged natural genetic variation between strains of C. elegans with differential responses to abamectin to identify three genomic regions on chromosome V, each containing one or more genes that contribute to ML resistance. Two of these loci have not been previously discovered and likely represent novel resistance mechanisms. We also compared the genes in these two novel loci to the genes found within genomic regions linked to ML resistance in the parasite Haemonchus contortus and found several cases of overlap between the two species. Overall, this study highlights the advantages of using C. elegans to understand anthelmintic resistance in parasitic nematodes.

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Maternal-effect lethal mutations on linkage group II of Caenorhabditis elegans.

Genetics ◽

10.1093/genetics/120.4.977 ◽

1988 ◽

Vol 120 (4) ◽

pp. 977-986

Author(s):

K J Kemphues ◽

M Kusch ◽

N Wolf

Keyword(s):

Caenorhabditis Elegans ◽

Linkage Group ◽

Maternal Effect ◽

Essential Genes ◽

The Other ◽

C Elegans ◽

Lethal Mutations ◽

Embryonic Lethal ◽

Embryonic Lethal Mutations ◽

F1 Progeny

Abstract We have analyzed a set of linkage group (LG) II maternal-effect lethal mutations in Caenorhabditis elegans isolated by a new screening procedure. Screens of 12,455 F1 progeny from mutagenized adults resulted in the recovery of 54 maternal-effect lethal mutations identifying 29 genes. Of the 54 mutations, 39 are strict maternal-effect mutations defining 17 genes. These 17 genes fall into two classes distinguished by frequency of mutation to strict maternal-effect lethality. The smaller class, comprised of four genes, mutated to strict maternal-effect lethality at a frequency close to 5 X 10(-4), a rate typical of essential genes in C. elegans. Two of these genes are expressed during oogenesis and required exclusively for embryogenesis (pure maternal genes), one appears to be required specifically for meiosis, and the fourth has a more complex pattern of expression. The other 13 genes were represented by only one or two strict maternal alleles each. Two of these are identical genes previously identified by nonmaternal embryonic lethal mutations. We interpret our results to mean that although many C. elegans genes can mutate to strict maternal-effect lethality, most genes mutate to that phenotype rarely. Pure maternal genes, however, are among a smaller class of genes that mutate to maternal-effect lethality at typical rates. If our interpretation is correct, we are near saturation for pure maternal genes in the region of LG II balanced by mnC1. We conclude that the number of pure maternal genes in C. elegans is small, being probably not much higher than 12.

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A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics

Scientific Reports ◽

10.1038/s41598-021-88150-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jessica Knox ◽

Nicolas Joly ◽

Edmond M. Linossi ◽

José A. Carmona-Negrón ◽

Natalia Jura ◽

...

Keyword(s):

Caenorhabditis Elegans ◽

Developmental Delay ◽

Small Molecule ◽

Parasitic Nematode ◽

Kinase Inhibitor ◽

Binding Pocket ◽

Drug Binding ◽

Nematode Infection ◽

Selective Inhibitors ◽

C Elegans

AbstractOver one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to the anthelmintics currently used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-selective manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode Caenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in C. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-selective inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.

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Immune responses of Texel sheep to excretory/secretory products of adult Haemonchus contortus

Parasitology ◽

10.1017/s0031182000076198 ◽

1994 ◽

Vol 108 (3) ◽

pp. 351-357 ◽

Cited By ~ 61

Author(s):

H. D. F. H. Schallig ◽

M. A. W. van Leeuwen ◽

W. M. L. Hendrikx

Keyword(s):

Immune Response ◽

Immune Responses ◽

Haemonchus Contortus ◽

Lymphocyte Proliferation ◽

The Other ◽

Proliferation Index ◽

Serum Samples ◽

Immunoblotting Analysis ◽

Molecular Weights ◽

Secretory Products

SUMMARYThe excretory/secretory (E/S) products of adult Haemonchus contortus comprise of at least 15 polypeptides with molecular weights ranging from 10 to > 100 kDa. These E/S products induce an immune response in infected Texel sheep, as demonstrated by specific IgGI levels and a significant lymphocyte proliferation index. Moreover, immunoblotting analysis revealed that sera of primary H. contortus-infected sheep specifically recognize a 24 kDa E/S product. In addition, sera of challenged sheep react strongly with a 15 kDa E/S product. The other E/S products of H. contortus showed immunoreactivity with serum samples of Haemonchus-infected sheep as well as with samples of sheep harbouring other trichostrongylid infections. These cross-reacting epitopes are the main cause of the lack of specificity of an E/S material- based ELISA. This ELISA can differentiate Haemonchus infections from Nematodirus battus infections, but not from Ostertagia circumcincta or Trichostrongylus colubriformis infections.

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Speciation of cestoda. Evidence for two sibling species in the complex Bothrimonus nylandicus (Schneider 1902) (Cestoda: Cyathocephalidea)

Parasitology ◽

10.1017/s0031182000066816 ◽

1988 ◽

Vol 97 (1) ◽

pp. 139-147 ◽

Cited By ~ 20

Author(s):

F. Renaud ◽

C. Gabrion

Keyword(s):

Sibling Species ◽

Definitive Host ◽

Parasite Species ◽

Adult Stage ◽

Life Cycles ◽

The Other ◽

Congeneric Species ◽

Biochemical Genetic ◽

Autumn And Winter ◽

Biological Differences

SUMMARYUsing biochemical genetic methods, we have distinguished 2 sibling species in the complex Bothrimonus nylandicus (Schneider, 1902), which infest 2 congeneric species of sole (Solea lascaris and Solea impar) on European coasts (Atlantic and Mediterranean). Neither of the parasite species is specific for either of the sole species, but one of them is present all year round, whereas the other is absent in the autumn and winter and only appears in the spring, subsequently disappearing at the end of the summer. Only S. impar lives in the Mediterranean, and is equally infested by both cestodes, whereas both species occur in the Atlantic and each of them is preferentially infested by 1 species of cestode. The shortness of the adult stage of the parasite in the definitive host and the presence of 2 life-cycles associated with competition between the 2 hosts in the Atlantic could be responsible for the biological differences observed and for maintaining the sibling species in sympatry.

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Two new inbred rat strains derived from SHR: WKHA, hyperactive, and WKHT, hypertensive, rats

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.1991.261.2.h583 ◽

1991 ◽

Vol 261 (2) ◽

pp. H583-H589 ◽

Cited By ~ 7

Author(s):

E. D. Hendley ◽

W. G. Ohlsson

Keyword(s):

The Other ◽

Hypertensive Rats ◽

Rat Strains ◽

Spontaneously Hypertensive ◽

Behavioral Profile ◽

Behavioral Abnormalities ◽

Inbred Rats ◽

Wistar Kyoto ◽

Inbred Rat ◽

Biological Differences

Two new strains of inbred rats have been developed. One, WKHA, exhibits hyperactivity, and the other, WKHT, exhibits hypertension. Both of these traits are expressed in the SHR. By crossing spontaneously hypertensive rats (SHRs) with Wistar-Kyoto (WKY) controls, followed by recombinant selected inbreeding, we succeeded in genetically separating the hyperactivity from the hypertension in two new strains. Longitudinal studies indicate a persistence of hypertension without hyperactivity in WKHTs, and hyperactivity without hypertension in WKHAs, over at least 1 year. Ventricular enlargement, another characteristic of SHRs, was observed in adult WKHTs after the onset of hypertension; however, ventricles were already enlarged in normotensive WKHAs at 6 wk. The emergent behavioral profile of WKHAs indicates that they retain the hyperactivity trait and hyperreactivity to stress, and not some of the other behaviors of SHRs, such as poor habituation. Studies in WKHTs suggest that they are an improvement over SHRs as a model of genetic hypertension as they lack some prominent behavioral abnormalities. Nevertheless, the four genetically related strains (WKHA, WKHT, SHR, and WKY), used together, are considered most appropriate for seeking correlations of biological differences with either hypertension or hyperactivity.

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Nematode ligand-gated chloride channels: an appraisal of their involvement in macrocyclic lactone resistance and prospects for developing molecular markers

Parasitology ◽

10.1017/s0031182007000042 ◽

2007 ◽

Vol 134 (8) ◽

pp. 1111-1121 ◽

Cited By ~ 51

Author(s):

S. McCAVERA ◽

T. K. WALSH ◽

A. J. WOLSTENHOLME

Keyword(s):

Haemonchus Contortus ◽

Chloride Channels ◽

Macrocyclic Lactone ◽

Parasitic Nematodes ◽

C Elegans ◽

Molecular Tests ◽

Cooperia Oncophora ◽

Macrocyclic Lactone Resistance ◽

High Level ◽

Laboratory Models

SUMMARYLigand-gated chloride channels, including the glutamate-(GluCl) and GABA-gated channels, are the targets of the macrocyclic lactone (ML) family of anthelmintics. Changes in the sequence and expression of these channels can cause resistance to the ML in laboratory models, such as Caenorhabditis elegans and Drosophila melanogaster. Mutations in multiple GluCl subunit genes are required for high-level ML resistance in C. elegans, and this can be influenced by additional mutations in gap junction and amphid genes. Parasitic nematodes have a different complement of channel subunit genes from C. elegans, but a few genes, including avr-14, are widely present. A polymorphism in an avr-14 orthologue, which makes the subunit less sensitive to ivermectin and glutamate, has been identified in Cooperia oncophora, and polymorphisms in several subunits have been reported from resistant isolates of Haemonchus contortus. This has led to suggestions that ML resistance may be polygenic. Possible reasons for this, and its consequences for the development of molecular tests for resistance, are explored.

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An Evolutionarily Conserved Pathway Essential for Orsay Virus Infection of Caenorhabditis elegans

mBio ◽

10.1128/mbio.00940-17 ◽

2017 ◽

Vol 8 (5) ◽

Cited By ~ 13

Author(s):

Hongbing Jiang ◽

Kevin Chen ◽

Luis E. Sandoval ◽

Christian Leung ◽

David Wang

Keyword(s):

Caenorhabditis Elegans ◽

Virus Infection ◽

Tyrosine Kinase ◽

Model Organism ◽

Wiskott Aldrich Syndrome ◽

C Elegans ◽

Evolutionarily Conserved ◽

Conserved Genes ◽

Orsay Virus ◽

Syndrome Protein

ABSTRACT Many fundamental biological discoveries have been made in Caenorhabditis elegans. The discovery of Orsay virus has enabled studies of host-virus interactions in this model organism. To identify host factors critical for Orsay virus infection, we designed a forward genetic screen that utilizes a virally induced green fluorescent protein (GFP) reporter. Following chemical mutagenesis, two Viro (virus induced reporter off) mutants that failed to express GFP were mapped to sid-3, a nonreceptor tyrosine kinase, and B0280.13 (renamed viro-2), an ortholog of human Wiskott-Aldrich syndrome protein (WASP). Both mutants yielded Orsay virus RNA levels comparable to that of the residual input virus, suggesting that they are not permissive for Orsay virus replication. In addition, we demonstrated that both genes affect an early prereplication stage of Orsay virus infection. Furthermore, it is known that the human ortholog of SID-3, activated CDC42-associated kinase (ACK1/TNK2), is capable of phosphorylating human WASP, suggesting that VIRO-2 may be a substrate for SID-3 in C. elegans. A targeted RNA interference (RNAi) knockdown screen further identified the C. elegans gene nck-1, which has a human ortholog that interacts with TNK2 and WASP, as required for Orsay virus infection. Thus, genetic screening in C. elegans identified critical roles in virus infection for evolutionarily conserved genes in a known human pathway. IMPORTANCE Orsay virus is the only known virus capable of naturally infecting the model organism Caenorhabditis elegans, which shares many evolutionarily conserved genes with humans. We exploited the robust genetic tractability of C. elegans to identify three host genes, sid-3, viro-2, and nck-1, which are essential for Orsay virus infection. Mutant animals that lack these three genes are highly defective in viral replication. Strikingly, the human orthologs of these three genes, activated CDC42-associated kinase (TNK2), Wiskott-Aldrich syndrome protein (WASP), and noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1) are part of a known signaling pathway in mammals. These results suggest that TNK2, WASP, and NCK1 may play important roles in mammalian virus infection. IMPORTANCE Orsay virus is the only known virus capable of naturally infecting the model organism Caenorhabditis elegans, which shares many evolutionarily conserved genes with humans. We exploited the robust genetic tractability of C. elegans to identify three host genes, sid-3, viro-2, and nck-1, which are essential for Orsay virus infection. Mutant animals that lack these three genes are highly defective in viral replication. Strikingly, the human orthologs of these three genes, activated CDC42-associated kinase (TNK2), Wiskott-Aldrich syndrome protein (WASP), and noncatalytic region of tyrosine kinase adaptor protein 1 (NCK1) are part of a known signaling pathway in mammals. These results suggest that TNK2, WASP, and NCK1 may play important roles in mammalian virus infection.

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