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Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici

Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of...

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Autores principales: McDonald, Megan C., McGinness, Lachlan, Hane, James K., Williams, Angela H., Milgate, Andrew, Solomon, Peter S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825649/
https://www.ncbi.nlm.nih.gov/pubmed/26837952
http://dx.doi.org/10.1534/g3.115.025197
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author McDonald, Megan C.
McGinness, Lachlan
Hane, James K.
Williams, Angela H.
Milgate, Andrew
Solomon, Peter S.
author_facet McDonald, Megan C.
McGinness, Lachlan
Hane, James K.
Williams, Angela H.
Milgate, Andrew
Solomon, Peter S.
author_sort McDonald, Megan C.
collection PubMed
description Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
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spelling pubmed-48256492016-04-11 Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici McDonald, Megan C. McGinness, Lachlan Hane, James K. Williams, Angela H. Milgate, Andrew Solomon, Peter S. G3 (Bethesda) Investigations Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene. Genetics Society of America 2016-01-29 /pmc/articles/PMC4825649/ /pubmed/26837952 http://dx.doi.org/10.1534/g3.115.025197 Text en Copyright © 2016 McDonald et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
McDonald, Megan C.
McGinness, Lachlan
Hane, James K.
Williams, Angela H.
Milgate, Andrew
Solomon, Peter S.
Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title_full Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title_fullStr Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title_full_unstemmed Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title_short Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici
title_sort utilizing gene tree variation to identify candidate effector genes in zymoseptoria tritici
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825649/
https://www.ncbi.nlm.nih.gov/pubmed/26837952
http://dx.doi.org/10.1534/g3.115.025197
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