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Zheng Y, Young ND, Campos T, Korhonen PK, Wang T, Sumanan S, Taki AC, Byrne JJ, Chang BCH, Song J, Gasser RB. Chromosome-contiguous genome for the Haecon-5 strain of Haemonchus contortus reveals marked genetic variability and enables the discovery of essential gene candidates. Int J Parasitol 2024:S0020-7519(24)00153-X. [PMID: 39168434 DOI: 10.1016/j.ijpara.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/24/2024] [Accepted: 08/10/2024] [Indexed: 08/23/2024]
Abstract
Millions of livestock animals worldwide are infected with the haematophagous barber's pole worm, Haemonchus contortus, the aetiological agent of haemonchosis. Despite the major significance of this parasite worldwide and its widespread resistance to current treatments, the lack of a high-quality genome for the well-defined strain of this parasite from Australia, called Haecon-5, has constrained research in a number of areas including host-parasite interactions, drug discovery and population genetics. To enable research in these areas, we report here a chromosome-contiguous genome (∼280 Mb) for Haecon-5 with high-quality models for 19,234 protein-coding genes. Comparative genomic analyses show significant genomic similarity (synteny) with a UK strain of H. contortus, called MHco3(ISE).N1 (abbreviated as "ISE"), but we also discover marked differences in genomic structure/gene arrangements, distribution of nucleotide variability (single nucleotide polymorphisms (SNPs) and indels) and orthology between Haecon-5 and ISE. We used the genome and extensive transcriptomic resources for Haecon-5 to predict a subset of essential single-copy genes employing a "cross-species" machine learning (ML) approach using a range of features from nucleotide/protein sequences, protein orthology, subcellular localisation, single-cell RNA-seq and/or histone methylation data available for the model organisms Caenorhabditis elegans and Drosophila melanogaster. From a set of 1,464 conserved single copy genes, transcribed in key life-cycle stages of H. contortus, we identified 232 genes whose homologs have critical functions in C. elegans and/or D. melanogaster, and prioritised 10 of them for further characterisation; nine of the 10 genes likely play roles in neurophysiological processes, germline, hypodermis and/or respiration, and one is an unknown (orphan) gene for which no detailed functional information exists. Future studies of these genes/gene products are warranted to elucidate their roles in parasite biology, host-parasite interplay and/or disease. Clearly, the present Haecon-5 reference genome and associated resources now underpin a broad range of fundamental investigations of H. contortus and could assist in accelerating the discovery of novel intervention targets and drug candidates to combat haemonchosis.
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Affiliation(s)
- Yuanting Zheng
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia.
| | - Tulio Campos
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K Korhonen
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Tao Wang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Sunita Sumanan
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Aya C Taki
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Joseph J Byrne
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Bill C H Chang
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Jiangning Song
- Faculty of IT, Department of Data Science and AI, Monash University, Victoria, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia; Monash Data Futures Institute, Monash University, Victoria, Australia.
| | - Robin B Gasser
- Department of Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia.
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Zadesenets KS, Ershov NI, Bondar NP, Rubtsov NB. Unraveling the Unusual Subgenomic Organization in the Neopolyploid Free-Living Flatworm Macrostomum lignano. Mol Biol Evol 2023; 40:msad250. [PMID: 37979163 PMCID: PMC10733133 DOI: 10.1093/molbev/msad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/21/2023] [Accepted: 11/14/2023] [Indexed: 11/20/2023] Open
Abstract
Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.
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Affiliation(s)
- Kira S Zadesenets
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Nikita I Ershov
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Natalia P Bondar
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolai B Rubtsov
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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Reiter T, Brooks† PT, Irber† L, Joslin† SEK, Reid† CM, Scott† C, Brown CT, Pierce-Ward NT. Streamlining data-intensive biology with workflow systems. Gigascience 2021; 10:giaa140. [PMID: 33438730 PMCID: PMC8631065 DOI: 10.1093/gigascience/giaa140] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/14/2022] Open
Abstract
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these practices in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.
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Affiliation(s)
- Taylor Reiter
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Phillip T Brooks†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Luiz Irber†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Shannon E K Joslin†
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles M Reid†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Camille Scott†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - N Tessa Pierce-Ward
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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Zadesenets KS, Rubtsov NB. Regions enriched for DNA repeats in chromosomes of Macrostomum mirumnovem, a species with a recent Whole Genome Duplication. Vavilovskii Zhurnal Genet Selektsii 2020; 24:636-642. [PMID: 33659849 PMCID: PMC7716556 DOI: 10.18699/vj20.657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The free-living flatworm Macrostomum mirumnovem is a neopolyploid species whose genome underwent
a recent Whole Genome Duplication (WGD). In the result of chromosome fusions of the ancient haploid
chromosome set, large metacentric chromosomes were formed. In addition to three pairs of small metacentrics,
the current karyotype of M. mirumnovem contains two pairs of large metacentric chromosomes, MMI1 and MMI2.
The generation of microdissected DNA libraries enriched for DNA repeats followed by DNA probe preparation and
fluorescent in situ hybridization (FISH) were performed. The DNA probes obtained marked chromosome regions
enriched for different DNA repeats in the M. mirumnovem chromosomes. The size and localization of these regions
varied in different copies of large chromosomes. They varied even in homologous chromosomes, suggesting their
divergence due to genome re-diploidization after a WGD. Besides the newly formed chromosome regions enriched
for DNA repeats, B chromosomes were found in the karyotypes of the studied specimens of M. mirumnovem. These
B chromosomes varied in size and morphology. FISH with microdissected DNA probes revealed that some Bs had
a distinct DNA content. FISH could paint differently B chromosomes in different worms and even in the same sample.
B chromosomes could carry a bright specific fluorescent signal or could show no fluorescent signal at all. In latter
cases, the specific FISH signal could be absent even in the pericentromeric region of the B chromosome. Possible
mechanisms of B chromosome formation and their further evolution are discussed. The results obtained indicate
an important role that repetitive DNAs play in genome re-diploidization initiating a rapid differentiation of large
chromosome copies. Taking together, karyotype peculiarities (a high level of intraspecific karyotypic diversity associated
with chromosome number variation, structural chromosomal rearrangements, and the formation of new
regions enriched for DNA repeats) and some phenotypic features of M. mirumnovem (small body size, short lifecycle,
easy maintenance in the laboratory) make this species a perspective model in the studies of genomic and
karyotypic evolution in species passed through a recent WGD event.
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Affiliation(s)
- K S Zadesenets
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N B Rubtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Sheng M, Gao M, Wang L, Ren X. Chromosome Microdissection and Microcloning: Technique and Application in the Plant Sciences. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Maoyin Sheng
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Mengdi Gao
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Linjiao Wang
- National Engineering Research Centre for Karst Rocky Desertification Control, Guizhou Normal University
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry
| | - Xuelian Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science
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