The genome of the emerging barley pathogen Ramularia collo-cygni

GRD McGrann, A Andongabo, E Sjokvist, U Trivedi, F Dussart, M Kaczmarek, A Mackenzie, JM Fountaine, JMG Taylor, LJ Paterson, K Gorniak, FJ Burnett, K Kanyuka, KE Hammond-Kosack, JJ Rudd, M Blaxter, ND Havis

Research output: Contribution to journalArticle

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Abstract

Background: Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results: The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1,053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions: The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph.
Original languageEnglish
Article number584
JournalBMC Genomics
Volume17
Issue number584
Early online date9 Aug 2016
DOIs
Publication statusFirst published - 9 Aug 2016

Fingerprint

Ramularia
Cygnus
barley
Mycosphaerellaceae
genome
pathogens
Dothideomycetes
enzymes
genes
plant pathogens
fungi
Capnodiales
pathogenesis
leaf spot
carbohydrates
endophytes
Ascomycota
secondary metabolites
complement
toxins

Bibliographical note

1030766

Keywords

  • Dothideomycetes
  • Endophyte
  • Necrotroph
  • Ramularia leaf spot
  • Rubellin toxin
  • Whole genome sequencing

Cite this

McGrann, GRD., Andongabo, A., Sjokvist, E., Trivedi, U., Dussart, F., Kaczmarek, M., ... Havis, ND. (2016). The genome of the emerging barley pathogen Ramularia collo-cygni. BMC Genomics, 17(584), [584]. https://doi.org/10.1186/s12864-016-2928-3
McGrann, GRD ; Andongabo, A ; Sjokvist, E ; Trivedi, U ; Dussart, F ; Kaczmarek, M ; Mackenzie, A ; Fountaine, JM ; Taylor, JMG ; Paterson, LJ ; Gorniak, K ; Burnett, FJ ; Kanyuka, K ; Hammond-Kosack, KE ; Rudd, JJ ; Blaxter, M ; Havis, ND. / The genome of the emerging barley pathogen Ramularia collo-cygni. In: BMC Genomics. 2016 ; Vol. 17, No. 584.
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McGrann, GRD, Andongabo, A, Sjokvist, E, Trivedi, U, Dussart, F, Kaczmarek, M, Mackenzie, A, Fountaine, JM, Taylor, JMG, Paterson, LJ, Gorniak, K, Burnett, FJ, Kanyuka, K, Hammond-Kosack, KE, Rudd, JJ, Blaxter, M & Havis, ND 2016, 'The genome of the emerging barley pathogen Ramularia collo-cygni', BMC Genomics, vol. 17, no. 584, 584. https://doi.org/10.1186/s12864-016-2928-3

The genome of the emerging barley pathogen Ramularia collo-cygni. / McGrann, GRD; Andongabo, A; Sjokvist, E; Trivedi, U; Dussart, F; Kaczmarek, M; Mackenzie, A; Fountaine, JM; Taylor, JMG; Paterson, LJ; Gorniak, K; Burnett, FJ; Kanyuka, K; Hammond-Kosack, KE; Rudd, JJ; Blaxter, M; Havis, ND.

In: BMC Genomics, Vol. 17, No. 584, 584, 09.08.2016.

Research output: Contribution to journalArticle

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T1 - The genome of the emerging barley pathogen Ramularia collo-cygni

AU - McGrann, GRD

AU - Andongabo, A

AU - Sjokvist, E

AU - Trivedi, U

AU - Dussart, F

AU - Kaczmarek, M

AU - Mackenzie, A

AU - Fountaine, JM

AU - Taylor, JMG

AU - Paterson, LJ

AU - Gorniak, K

AU - Burnett, FJ

AU - Kanyuka, K

AU - Hammond-Kosack, KE

AU - Rudd, JJ

AU - Blaxter, M

AU - Havis, ND

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N2 - Background: Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results: The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1,053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions: The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph.

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KW - Dothideomycetes

KW - Endophyte

KW - Necrotroph

KW - Ramularia leaf spot

KW - Rubellin toxin

KW - Whole genome sequencing

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JO - BMC Genomics

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McGrann GRD, Andongabo A, Sjokvist E, Trivedi U, Dussart F, Kaczmarek M et al. The genome of the emerging barley pathogen Ramularia collo-cygni. BMC Genomics. 2016 Aug 9;17(584). 584. https://doi.org/10.1186/s12864-016-2928-3