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Cantacessi C, Mitreva M, Campbell BE, Hall RS, Young ND, Jex AR, Ranganathan S, Gasser RB. First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2010; 10:1199-207. [PMID: 20692378 PMCID: PMC3666958 DOI: 10.1016/j.meegid.2010.07.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 07/29/2010] [Indexed: 12/22/2022]
Abstract
Trichostrongylus colubriformis (Strongylida), a small intestinal nematode of small ruminants, is a major cause of production and economic losses in many countries. The aims of the present study were to define the transcriptome of the adult stage of T. colubriformis, using 454 sequencing technology and bioinformatic analyses, and to predict the main pathways that key groups of molecules are linked to in this nematode. A total of 21,259 contigs were assembled from the sequence data produced from a normalized cDNA library; 7876 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and encoded, amongst others, proteins with 'transthyretin-like' (8.8%), 'RNA recognition' (8.4%) and 'metridin-like ShK toxin' (7.6%) motifs. Bioinformatic analyses inferred that relatively high proportions of the C. elegans homologues are involved in biological pathways linked to 'peptidases' (4%), 'ribosome' (3.6%) and 'oxidative phosphorylation' (3%). Highly represented were peptides predicted to be associated with the nervous system, digestion of host proteins or inhibition of host proteases. Probabilistic functional gene networking of the complement of C. elegans orthologues (n=2126) assigned significance to particular subsets of molecules, such as protein kinases and serine/threonine phosphatases. The present study represents the first, comprehensive insight into the transcriptome of adult T. colubriformis, which provides a foundation for fundamental studies of the molecular biology and biochemistry of this parasitic nematode as well as prospects for identifying targets for novel nematocides. Future investigations should focus on comparing the transcriptomes of different developmental stages, both genders and various tissues of this parasitic nematode for the prediction of essential genes/gene products that are specific to nematodes.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Makedonka Mitreva
- Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, Forest Park Boulevard, St. Louis, Missouri, USA
| | - Bronwyn E. Campbell
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Ross S. Hall
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Aaron R. Jex
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Robin B. Gasser
- Department of Veterinary Science, The University of Melbourne, Werribee, Victoria, Australia
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Cantacessi C, Jex AR, Hall RS, Young ND, Campbell BE, Joachim A, Nolan MJ, Abubucker S, Sternberg PW, Ranganathan S, Mitreva M, Gasser RB. A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. Nucleic Acids Res 2010; 38:e171. [PMID: 20682560 PMCID: PMC2943614 DOI: 10.1093/nar/gkq667] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/11/2010] [Accepted: 07/15/2010] [Indexed: 11/14/2022] Open
Abstract
Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Aaron R. Jex
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Ross S. Hall
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Neil D. Young
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Bronwyn E. Campbell
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Anja Joachim
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Matthew J. Nolan
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Sahar Abubucker
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Paul W. Sternberg
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Shoba Ranganathan
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Makedonka Mitreva
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Robin B. Gasser
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia, Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria, Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, MO 63108, Biology Division, California Institute of Technology, CA 91125, USA and Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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