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

^*Corresponding author for this work

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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 - 1 Mar 2016

Keywords

Helminth
nematode
genome
Strongyloides
Parastrongyloides
Rhabditophanes
parasitism
transcriptome
proteome
synteny
astacins
SCP/TAPS
gene clusters

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/ng.3495

Main_textAccepted author manuscript, 1.09 MBLicence: 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

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title = "The genomic basis of parasitism in the Strongyloides clade of nematodes",

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.",

keywords = "Helminth, nematode, genome, Strongyloides, Parastrongyloides, Rhabditophanes, parasitism, transcriptome, proteome, synteny, astacins, SCP/TAPS, gene clusters",

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

year = "2016",

month = mar,

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doi = "10.1038/ng.3495",

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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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T1 - The genomic basis of parasitism in the Strongyloides clade of nematodes

AU - Hunt, Vicky L.

AU - Tsai, Isheng J.

AU - Coghlan, Avril

AU - Reid, Adam J.

AU - Holroyd, Nancy

AU - Foth, Bernardo J.

AU - Tracey, Alan

AU - Cotton, James A.

AU - Stanley, Eleanor J.

AU - Beasley, Helen

AU - Bennett, Hayley M.

AU - Brooks, Karen

AU - Harsha, Bhavana

AU - Kajitani, Rei

AU - Kulkarni, Arpita

AU - Harbecke, Dorothee

AU - Nagayasu, Eiji

AU - Nichol, Sarah

AU - Ogura, Yoshitoshi

AU - Quail, Michael A.

AU - Randle, Nadine

AU - Xia, Dong

AU - Brattig, Norbert W.

AU - Soblik, Hanns

AU - Ribeiro, Diogo M.

AU - Sanchez-Flores, Alejandro

AU - Hayashi, Tetsuya

AU - Itoh, Takehiko

AU - Denver, Dee R.

AU - Grant, Warwick

AU - Stoltzfus, Jonathan D.

AU - Lok, James B.

AU - Murayama, Haruhiko

AU - Wastling, Jonathan

AU - Streit, Adrian

AU - Kikuchi, Taisei

AU - Viney, Mark

AU - Berriman, Matthew

PY - 2016/3/1

Y1 - 2016/3/1

N2 - 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.

AB - 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.

KW - Helminth

KW - nematode

KW - genome

KW - Strongyloides

KW - Parastrongyloides

KW - Rhabditophanes

KW - parasitism

KW - transcriptome

KW - proteome

KW - synteny

KW - astacins

KW - SCP/TAPS

KW - gene clusters

UR - http://www.scopus.com/inward/record.url?scp=84959527280&partnerID=8YFLogxK

U2 - 10.1038/ng.3495

DO - 10.1038/ng.3495

M3 - Article (Academic Journal)

C2 - 26829753

AN - SCOPUS:84959527280

SN - 1061-4036

VL - 48

SP - 299

EP - 307

JO - Nature Genetics

JF - Nature Genetics

IS - 3

ER -

The genomic basis of parasitism in the Strongyloides clade of nematodes

Abstract

Keywords

UN SDGs

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