The genomic basis of parasitism in the Strongyloides clade of nematodes

Vicky L. Hunt; Isheng J. Tsai; Avril Coghlan; Adam J. Reid; Nancy Holroyd; Bernardo J. Foth; Alan Tracey; James A. Cotton; Eleanor J. Stanley; Helen Beasley; Hayley M. Bennett; Karen Brooks; Bhavana Harsha; Rei Kajitani; Arpita Kulkarni; Dorothee Harbecke; Eiji Nagayasu; Sarah Nichol; Yoshitoshi Ogura; Michael A. Quail; Nadine Randle; Dong Xia; Norbert W. Brattig; Hanns Soblik; Diogo M. Ribeiro; Alejandro Sanchez-Flores; Tetsuya Hayashi; Takehiko Itoh; Dee R. Denver; Warwick Grant; Jonathan D. Stoltzfus; James B. Lok; Haruhiko Murayama; Jonathan Wastling; Adrian Streit; Taisei Kikuchi; Mark Viney; Matthew Berriman

doi:10.1038/ng.3495

The genomic basis of parasitism in the Strongyloides clade of nematodes

Vicky L. Hunt, Isheng J. Tsai, Avril Coghlan, Adam J. Reid, Nancy Holroyd, Bernardo J. Foth, Alan Tracey, James A. Cotton, Eleanor J. Stanley, Helen Beasley, Hayley M. Bennett, Karen Brooks, Bhavana Harsha, Rei Kajitani, Arpita Kulkarni, Dorothee Harbecke, Eiji Nagayasu, Sarah Nichol, Yoshitoshi Ogura, Michael A. QuailNadine Randle, Dong Xia, Norbert W. Brattig, Hanns Soblik, Diogo M. Ribeiro, Alejandro Sanchez-Flores, Tetsuya Hayashi, Takehiko Itoh, Dee R. Denver, Warwick Grant, Jonathan D. Stoltzfus, James B. Lok, Haruhiko Murayama, Jonathan Wastling, Adrian Streit, Taisei Kikuchi, Mark Viney, Matthew Berriman

Department of Life Sciences

Research output: Contribution to journal › Article › peer-review

188 Citations (SciVal)

Abstract

Soil-transmitted nematodes, including the Strongyloides genus, cause one of the most prevalent neglected tropical diseases. Here we compare the genomes of four Strongyloides species, including the human pathogen Strongyloides stercoralis, and their close relatives that are facultatively parasitic (Parastrongyloides trichosuri) and free-living (Rhabditophanes sp. KR3021). A significant paralogous expansion of key gene families - families encoding astacin-like and SCP/TAPS proteins - is associated with the evolution of parasitism in this clade. Exploiting the unique Strongyloides life cycle, we compare the transcriptomes of the parasitic and free-living stages and find that these same gene families are upregulated in the parasitic stages, underscoring their role in nematode parasitism.

Original language	English
Pages (from-to)	299-307
Number of pages	9
Journal	Nature Genetics
Volume	48
Issue number	3
Early online date	1 Feb 2016
DOIs	https://doi.org/10.1038/ng.3495
Publication status	Published - 13 Mar 2016

Funding

We thank, from the Wellcome Trust Sanger Institute, C. Griffiths, D. Willey, R. Rance and DNA Pipelines; J. Keane and D. Gordon for bioinformatics support; M. Dunn for the S. venezuelensis optical map; A. Babbage for laboratory support; and M. Zarowiecki for gene finding and functional annotation advice. We thank for technical help L. Hughes and L. Weldon (University of Bristol); H. Massey, Jr., X. Li and H. Shao (University of Pennsylvania); D.K. Howe and R.I. Wernick (Oregon State University); H. Denise (European Bioinformatics Institute); M. Yabana (Tokyo Institute of Technology); and A. Hino and R. Tanaka (University of Miyazaki) and A. Toyoda (National Institute of Genetics) for sequencing. The S. ratti transcriptome and proteome work was funded by Wellcome Trust grant 094462/Z/10/Z awarded to M.V., J.W. and M.B. The S. ratti, S. stercoralis, S. papillosus, P. trichosuri and Rhabditophanes sp. KR3021 genome sequencing and the S. venezuelensis optical mapping were funded by Wellcome Trust grant 098051. The S. venezuelensis work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI (24310142, 21590466 and 24780044), KAKENHI for Innovative Areas ‘Genome Science’ (221S0002) and the Integrated Research Project for Human and Veterinary Medicine of the University of Miyazaki. I.J.T. was supported by Academia Sinica. Work was funded by grants AI050668 and AI105856 from the US National Institutes of Health (NIH) to J.B.L. and by Resource-Related Research Grant RR02512 from the US NIH to M. Haskins, which provided research materials for the study. J.D.S. received support from US NIH training grant AI060516. A.K. was supported by a predoctoral stipend from the Max Planck Society. Work by A.K., D.H. and A.S. was funded by the Max Planck Society.

ASJC Scopus subject areas

Genetics

UN SDGs

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10.1038/ng.3495Licence: CC BY-NC-SA

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Hunt, V. L., Tsai, I. J., Coghlan, A., Reid, A. J., Holroyd, N., Foth, B. J., Tracey, A., Cotton, J. A., Stanley, E. J., Beasley, H., Bennett, H. M., Brooks, K., Harsha, B., Kajitani, R., Kulkarni, A., Harbecke, D., Nagayasu, E., Nichol, S., Ogura, Y., ... Berriman, M. (2016). The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics, 48(3), 299-307. https://doi.org/10.1038/ng.3495

Hunt, VL, Tsai, IJ, Coghlan, A, Reid, AJ, Holroyd, N, Foth, BJ, Tracey, A, Cotton, JA, Stanley, EJ, Beasley, H, Bennett, HM, Brooks, K, Harsha, B, Kajitani, R, Kulkarni, A, Harbecke, D, Nagayasu, E, Nichol, S, Ogura, Y, Quail, MA, Randle, N, Xia, D, Brattig, NW, Soblik, H, Ribeiro, DM, Sanchez-Flores, A, Hayashi, T, Itoh, T, Denver, DR, Grant, W, Stoltzfus, JD, Lok, JB, Murayama, H, Wastling, J, Streit, A, Kikuchi, T, Viney, M & Berriman, M 2016, 'The genomic basis of parasitism in the Strongyloides clade of nematodes', Nature Genetics, vol. 48, no. 3, pp. 299-307. https://doi.org/10.1038/ng.3495

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AU - Lok, James B.

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The genomic basis of parasitism in the Strongyloides clade of nematodes

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Vicky Hunt

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The genomic basis of parasitism in the Strongyloides clade of nematodes

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