title: Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes.
abstract: The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Narayana M
authors.initials: NM
authors.lastname: Upadhyaya
authors.affiliation: Research School of Biology, Australian National University Canberra, ACT, Australia.
authors.forename: Diana P
authors.initials: DP
authors.lastname: Garnica
authors.affiliation: Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.
authors.forename: Haydar
authors.initials: H
authors.lastname: Karaoglu
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Jana
authors.initials: J
authors.lastname: Sperschneider
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Adnane
authors.initials: A
authors.lastname: Nemri
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Bo
authors.initials: B
authors.lastname: Xu
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Rohit
authors.initials: R
authors.lastname: Mago
authors.affiliation: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard Cambridge, MA, USA.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Cuomo
authors.affiliation: Research School of Biology, Australian National University Canberra, ACT, Australia.
authors.forename: John P
authors.initials: JP
authors.lastname: Rathjen
authors.affiliation: Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney Narellan, NSW, Australia.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Park
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Ellis
authors.affiliation: Agriculture Flagship, Commonwealth Scientific and Industrial Research Organization Canberra, ACT, Australia.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Dodds
keywords: avirulence; effectors; haustoria; resistance; secreted proteins