title: Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.
abstract: BACKGROUND
  Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt).
  
  
  RESULTS
  The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors.
  
  
  CONCLUSIONS
  Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen's ability to infect the host.
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.|USDA-ARS, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
authors.forename: William B
authors.initials: WB
authors.lastname: Rutter
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Andres
authors.initials: A
authors.lastname: Salcedo
authors.affiliation: Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Alina
authors.initials: A
authors.lastname: Akhunova
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: He
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.|TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, 101 Gateway, Suite A, College Station, TX, 77845, USA.
authors.forename: Shichen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Integrated Genomics Facility, Kansas State University, Manhattan, KS, 66506, USA.|School of Data and Computer Science, Sun Yat-sen University, Guangzhou, 510006, China.
authors.forename: Hanquan
authors.initials: H
authors.lastname: Liang
authors.affiliation: USDA ARS, Hard Winter Wheat Genetics Research Unit, Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Bowden
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. eakhunov@ksu.edu.
authors.forename: Eduard
authors.identifier: http://orcid.org/0000-0002-0416-5211
authors.initials: E
authors.lastname: Akhunov
mesh_terms: D001483:Base Sequence; D001487:Basidiomycota / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D054884:Host-Pathogen Interactions; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D018515:Plant Leaves / Q000235:genetics / Q000382:microbiology; D010940:Plant Proteins / Q000235:genetics*; D018547:Plant Stems / Q000235:genetics / Q000382:microbiology; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
chemical_list: D010940:Plant Proteins
keywords: Comparative genomics; Gene co-expression network; Stem rust; Wheat resistance