title: Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici.
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.
authors.affiliation: Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 2601.
authors.forename: Megan C
authors.initials: MC
authors.lastname: McDonald
authors.affiliation: Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 2601.
authors.forename: Lachlan
authors.initials: L
authors.lastname: McGinness
authors.affiliation: Black Box Bioinformatics, Perth, WA, Australia 6102 CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia Curtin Institute for Computation, Curtin University, Perth, WA, Australia 6102.
authors.forename: James K
authors.initials: JK
authors.lastname: Hane
authors.affiliation: Black Box Bioinformatics, Perth, WA, Australia 6102 CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.
authors.forename: Angela H
authors.initials: AH
authors.lastname: Williams
authors.affiliation: NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, NSW, Australia 2795.
authors.forename: Andrew
authors.initials: A
authors.lastname: Milgate
authors.affiliation: Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia 2601 peter.solomon@anu.edu.au.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Solomon
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D015825:Chromosomes, Fungal; D005800:Genes, Fungal; D056726:Genetic Association Studies; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D016366:Open Reading Frames; D010641:Phenotype; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D014908:Triticum / Q000382:microbiology; D014774:Virulence / Q000235:genetics
keywords: Mycosphaerella graminicola; accessory chromosome; comparative genomics; fungal effector; intraspecific
references.citation: Plant Physiol. 2011 Jun;156(2):756-69
references.pmid: 21467214
references.citation: Annu Rev Phytopathol. 2008;46:75-100
references.pmid: 18680424
references.citation: PLoS Pathog. 2012 Sep;8(9):e1002893
references.pmid: 23028308
references.citation: PLoS Pathog. 2015 Jul;11(7):e1005055
references.pmid: 26225424
references.citation: Appl Environ Microbiol. 2008 Jun;74(12):3849-56
references.pmid: 18408061
references.citation: Nature. 2005 Apr 21;434(7036):980-6
references.pmid: 15846337
references.citation: PLoS Pathog. 2009 Sep;5(9):e1000581
references.pmid: 19806176
references.citation: PLoS Pathog. 2010;6(11):e1001180
references.pmid: 21079787
references.citation: Curr Biol. 2011 Dec 6;21(23):2017-22
references.pmid: 22100062
references.citation: Front Plant Sci. 2014 Sep 15;5:450
references.pmid: 25309551
references.citation: PLoS Pathog. 2012 Sep;8(9):e1002952
references.pmid: 23028337
references.citation: Mol Plant Pathol. 2011 Jun;12(5):413-24
references.pmid: 21535348
references.citation: Mol Plant Pathol. 2005 Sep 1;6(5):527-40
references.pmid: 20565677
references.citation: Mol Plant Pathol. 2009 Nov;10(6):735-47
references.pmid: 19849781
references.citation: Bioinformatics. 2012 Aug 15;28(16):2097-105
references.pmid: 22668792
references.citation: PLoS Pathog. 2011 Jul;7(7):e1002147
references.pmid: 21829350
references.citation: Nat Protoc. 2007;2(4):953-71
references.pmid: 17446895
references.citation: PLoS One. 2012;7(12):e49904
references.pmid: 23236356
references.citation: Trends Plant Sci. 2015 Apr;20(4):246-55
references.pmid: 25682011
references.citation: Genome Res. 2011 Dec;21(12):2157-66
references.pmid: 21994252
references.citation: Bioinformatics. 2015 Apr 15;31(8):1169-75
references.pmid: 25504847
references.citation: Bioinformatics. 2014 Aug 1;30(15):2114-20
references.pmid: 24695404
references.citation: Fungal Genet Biol. 2015 Jun;79:3-7
references.pmid: 26092782
references.citation: BMC Genomics. 2013;14:887
references.pmid: 24341723
references.citation: PLoS Genet. 2013 Jun;9(6):e1003567
references.pmid: 23785303
references.citation: Annu Rev Phytopathol. 2009;47:233-63
references.pmid: 19400631
references.citation: PLoS Pathog. 2012;8(4):e1002608
references.pmid: 22570606
references.citation: PLoS Pathog. 2012 Jan;8(1):e1002467
references.pmid: 22241993
references.citation: Nat Rev Genet. 2010 Aug;11(8):539-48
references.pmid: 20585331
references.citation: Fungal Genet Biol. 2015 Jun;79:71-5
references.pmid: 26092791
references.citation: PLoS Genet. 2011 Jun;7(6):e1002070
references.pmid: 21695235
references.citation: Mol Plant Pathol. 2015 Dec;16(9):931-45
references.pmid: 25727413
references.citation: Fungal Genet Biol. 2015 Jun;79:33-41
references.pmid: 26092788
references.citation: BMC Genomics. 2013;14:119
references.pmid: 23432788
references.citation: Mol Plant Microbe Interact. 2011 Jul;24(7):808-18
references.pmid: 21644839
references.citation: Phytopathology. 2013 Jul;103(7):666-72
references.pmid: 23384861
references.citation: Mol Biol Evol. 2007 Feb;24(2):398-411
references.pmid: 17095534
references.citation: Fungal Genet Biol. 2015 Jun;79:29-32
references.pmid: 26092787
references.citation: Genome Biol Evol. 2014 Jun;6(6):1353-65
references.pmid: 24920004
references.citation: Phytopathology. 2002 Apr;92(4):439-45
references.pmid: 18942957
references.citation: Nucleic Acids Res. 2004;32(5):1792-7
references.pmid: 15034147
references.citation: Mol Plant Microbe Interact. 2009 Feb;22(2):115-22
references.pmid: 19132864
references.citation: Mol Ecol. 2005 Jun;14(7):1881-96
references.pmid: 15910313
references.citation: Mol Plant Pathol. 2012 May;13(4):414-30
references.pmid: 22471698
references.citation: Mol Plant Microbe Interact. 1995 Jan-Feb;8(1):41-8
references.pmid: 7772802
references.citation: Fly (Austin). 2012 Apr-Jun;6(2):80-92
references.pmid: 22728672
references.citation: PLoS One. 2009;4(6):e5863
references.pmid: 19516898
references.citation: PLoS Pathog. 2015 May;11(5):e1004806
references.pmid: 26020524
references.citation: PLoS Comput Biol. 2014 Apr;10(4):e1003537
references.pmid: 24722319
references.citation: Phytopathology. 2014 Sep;104(9):985-92
references.pmid: 24624955
references.citation: New Phytol. 2013 Jul;199(1):241-51
references.pmid: 23550706
references.citation: PLoS Genet. 2012;8(8):e1002869
references.pmid: 22876203
references.citation: J Comput Biol. 2012 May;19(5):455-77
references.pmid: 22506599
references.citation: Mol Plant Microbe Interact. 2007 Feb;20(2):178-93
references.pmid: 17313169
references.citation: G3 (Bethesda). 2013 Jan;3(1):41-63
references.pmid: 23316438
references.citation: Fungal Genet Biol. 2015 Jun;79:54-62
references.pmid: 26092790
references.citation: Fungal Genet Biol. 2004 Feb;41(2):226-38
references.pmid: 14732268
references.citation: Plant Physiol. 2015 Mar;167(3):1158-85
references.pmid: 25596183