title: Transcriptome sequencing uncovers the Avr5 avirulence gene of the tomato leaf mold pathogen Cladosporium fulvum.
abstract: The Cf-5 gene of tomato confers resistance to strains of the fungal pathogen Cladosporium fulvum carrying the avirulence gene Avr5. Although Cf-5 has been cloned, Avr5 has remained elusive. We report the cloning of Avr5 using a combined bioinformatic and transcriptome sequencing approach. RNA-Seq was performed on the sequenced race 0 strain (0WU; carrying Avr5), as well as a race 5 strain (IPO 1979; lacking a functional Avr5 gene) during infection of susceptible tomato. Forty-four in planta-induced C. fulvum candidate effector (CfCE) genes of 0WU were identified that putatively encode a secreted, small cysteine-rich protein. An expressed transcript sequence comparison between strains revealed two polymorphic CfCE genes in IPO 1979. One of these conferred avirulence to IPO 1979 on Cf-5 tomato following complementation with the corresponding 0WU allele, confirming identification of Avr5. Complementation also led to increased fungal biomass during infection of susceptible tomato, signifying a role for Avr5 in virulence. Seven of eight race 5 strains investigated escape Cf-5-mediated resistance through deletion of the Avr5 gene. Avr5 is heavily flanked by repetitive elements, suggesting that repeat instability, in combination with Cf-5-mediated selection pressure, has led to the emergence of race 5 strains deleted for the Avr5 gene.
authors.forename: Carl H
authors.initials: CH
authors.lastname: Mesarich
authors.forename: Scott A
authors.initials: SA
authors.lastname: Griffiths
authors.forename: Ate
authors.initials: A
authors.lastname: van der Burgt
authors.forename: Bilal
authors.initials: B
authors.lastname: Okmen
authors.forename: Henriek G
authors.initials: HG
authors.lastname: Beenen
authors.forename: Desalegn W
authors.initials: DW
authors.lastname: Etalo
authors.forename: Matthieu H A J
authors.initials: MH
authors.lastname: Joosten
authors.forename: Pierre J G M
authors.initials: PJ
authors.lastname: de Wit
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D002963:Cladosporium / Q000235:genetics* / Q000472:pathogenicity; D003001:Cloning, Molecular; D019295:Computational Biology; D005656:Fungal Proteins / Q000235:genetics*; D017353:Gene Deletion; D015966:Gene Expression Regulation, Fungal; D005816:Genetic Complementation Test; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000276:immunology / Q000382:microbiology*; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism; D010935:Plant Diseases / Q000276:immunology / Q000382:microbiology*; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014774:Virulence; D037521:Virulence Factors
chemical_list: D005656:Fungal Proteins; D012331:RNA, Fungal; D037521:Virulence Factors; D009584:Nitrogen