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

G3 : Genes - Genomes - Genetics
Megan C McDonaldPeter S Solomon

Abstract

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.

References

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Citations

Oct 25, 2016·Molecular Ecology·Daniel Croll, Bruce A McDonald
Oct 6, 2017·Molecular Biology and Evolution·Fanny E Hartmann, Daniel Croll
Oct 20, 2017·Genome Biology and Evolution·Baojun WuWeilong Hao
Nov 1, 2016·MBio·Clémence PlissonneauDaniel Croll
Dec 12, 2018·Applied and Environmental Microbiology·Megan C McDonaldAndrew Milgate
Apr 22, 2020·Chemistry : a European Journal·Zhao-Qing LiuXiao-Tong Wang
Jan 27, 2019·Ecology and Evolution·Janine HaueisenEva H Stukenbrock

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Datasets Mentioned

BETA
PRJNA299857

Methods Mentioned

BETA
RNA-seq

Software Mentioned

Picard
VariantFiltration
GATK
R
PhyBi
popart
BLAST
DensiTree
Newick
Densi Tree

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