title: Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.
abstract: Three members of thePucciniagenus,Pucciniatriticina(Pt),Pstriiformisf.sp.tritici(Pst), andPgraminisf.sp.tritici(Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes ofPtandPstwere sequenced and compared to that ofPgtto identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection.Pthad the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% forPstand 36.5% forPgtWe find all three genomes are highly heterozygous, withPst[5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected inPt(2.57 SNPs/kb) and that previously reported forPgtOf 1358 predicted effectors inPt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryoticPucciniaspecies along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologousUstilago maydismating assay and host-induced gene silencing (HIGS) of the HD andSTE3alleles reduced wheat host infection.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.
authors.forename: Christina A
authors.identifier: 0000-0002-5778-960X
authors.initials: CA
authors.lastname: Cuomo
authors.affiliation: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.
authors.forename: Guus
authors.identifier: 0000-0002-3065-6989
authors.initials: G
authors.lastname: Bakkeren
authors.affiliation: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada.
authors.forename: Hala Badr
authors.initials: HB
authors.lastname: Khalil
authors.affiliation: Agriculture and Agri-Food Canada, Morden Research and Development Centre, Manitoba R6M 1Y5, Canada.
authors.forename: Vinay
authors.initials: V
authors.lastname: Panwar
authors.affiliation: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Joly
authors.affiliation: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada.
authors.forename: Rob
authors.initials: R
authors.lastname: Linning
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Sharadha
authors.initials: S
authors.lastname: Sakthikumar
authors.affiliation: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada.
authors.forename: Xiao
authors.initials: X
authors.lastname: Song
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Goldberg
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: The Institute for Cereal Crops Improvement, Tel Aviv University, Ramat Aviv 69978, Israel.
authors.forename: Yehoshua
authors.initials: Y
authors.lastname: Anikster
authors.affiliation: Department of Plant Pathology, Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas 66506.
authors.forename: Myron
authors.initials: M
authors.lastname: Bruce
authors.affiliation: Department of Plant Pathology, Washington State University, Pullman, Washington 99164.
authors.forename: Meinan
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Plant Pathology, Washington State University, Pullman, Washington 99164.
authors.forename: Chuntao
authors.initials: C
authors.lastname: Yin
authors.affiliation: Agriculture and Agri-Food Canada, Morden Research and Development Centre, Manitoba R6M 1Y5, Canada.
authors.forename: Brent
authors.initials: B
authors.lastname: McCallum
authors.affiliation: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108.
authors.forename: Les J
authors.initials: LJ
authors.lastname: Szabo
authors.affiliation: Department of Plant Pathology, Washington State University, Pullman, Washington 99164.
authors.forename: Scot
authors.initials: S
authors.lastname: Hulbert
authors.affiliation: Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture-Agricultural Research Service, Pullman, Washington 99164.
authors.forename: Xianming
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Plant Pathology, Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas 66506 cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.
authors.forename: John P
authors.identifier: 0000-0003-3872-2909
authors.initials: JP
authors.lastname: Fellers
mesh_terms: D001487:Basidiomycota / Q000235:genetics* / Q000472:pathogenicity; D049770:Genes, Mating Type, Fungal / Q000235:genetics; D016681:Genome, Fungal; D008018:Life Cycle Stages / Q000235:genetics; D058977:Molecular Sequence Annotation; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D043563:Receptors, Pheromone / Q000235:genetics; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics / Q000254:growth & development / Q000382:microbiology*
chemical_list: D043563:Receptors, Pheromone
keywords: Puccinia; effectors; genome comparisons; mating-type genes; sexual stage