Abstract
Pyrenophora teres f. teres is the causal agent of net form net blotch of barley. P. teres f. teres is prevalent globally across all barley growing regions and globally is the most devastating foliar disease of barley. Though economically important, the molecular mechanism whereby P. teres f. teres causes disease is poorly understood and investigations into these mechanisms have been hindered by a lack of genomic resources. To set a genomic foundation for P. teres f. teres the reference isolate 0-1 was sequenced and assembled using PacBio single molecule real-time (SMRT) sequencing and scaffolded into 12 chromosomes to provide the first finished genome of P. teres f. teres. High confidence gene models were generated for the reference genome of isolate 0-1 using a combination of pure culture and in planta RNA sequencing. An additional four P. teres f. teres isolates were sequenced and assembled to the same quality as the reference isolate 0-1 and used in a comparative genomic study. Comparisons of the five P. teres f. teres isolates showed a two-speed genome architecture with the genome being partitioned into core and accessory genomic compartments. Accessory genomic compartments clustered in sub-telomeric regions of the P. teres f. teres genome with a majority of previously identified quantitative trait loci (QTL) associated with avirulence/virulence being spanned by these accessory regions. Using these genomic resources, with a bi-parental mapping population and a natural population for QTL analysis and genome wide association study (GWAS), respectively, we identified a candidate gene for the previously mapped AvrHar. QTL analysis identified a locus extending off the end of P. teres f. teres chromosome 5 and GWAS analysis identified significant associations with a gene encoding a small secreted protein. The candidate AvrHar gene was validated using CRISPR-Cas9-RNP gene disruption in parental isolates 15A and 0-1. Disruption of AvrHar in isolate 15A did not result in a phenotypic change while disruption of the 0-1 allele resulted in a complete loss of pathogenicity. This is the first identification of an effector from P. teres f. teres validated using CRISPR-Cas9-RNP gene editing.
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Claims 9
Claim · model-written summary
The five P. teres f. teres isolates show a two-speed genome architecture with core and accessory compartments.
- Taxon
- barley
.jpg?width=60)
Hordeum vulgaree0 - Interactor
- P. teres f. teres
Pyrenophora teres f. terese1pathogen - Outcome
- two-speed genome architecturee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e1“Comparisons of the five P. teres f. teres isolates showed a two-speed genome architecture with the genome being partitioned into core and accessory genomic compartments”
Claim · model-written summary
Accessory genomic compartments cluster in sub-telomeric regions of the P. teres f. teres genome.
- Taxon
- barleyHordeum vulgaree0
- Interactor
- P. teres f. teresPyrenophora teres f. terese2pathogen
- Outcome
- Accessory genomic compartments clustered in sub-telomeric regionse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e2“Accessory genomic compartments clustered in sub-telomeric regions of the P. teres f. teres genome”
Claim · model-written summary
A majority of previously identified QTL for avirulence/virulence are spanned by the accessory genomic regions.
- Taxon
- barleyHordeum vulgaree0
- Gene
- quantitative trait loci (QTL)e3
- Outcome
- being spanned by these accessory regionse3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e3“a majority of previously identified quantitative trait loci (QTL) associated with avirulence/virulence being spanned by these accessory regions”
Claim · model-written summary
QTL analysis identified a locus extending off the end of P. teres f. teres chromosome 5.
- Taxon
- barleyHordeum vulgaree0
- Interactor
- P. teres f. teresPyrenophora teres f. terese4pathogen
- Outcome
- a locus extending off the end of P. teres f. teres chromosome 5e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e4“QTL analysis identified a locus extending off the end of P. teres f. teres chromosome 5”
Claim · model-written summary
GWAS identified significant associations with a gene encoding a small secreted protein.
- Taxon
- barleyHordeum vulgaree0
- Gene
- a gene encoding a small secreted proteine5
- Outcome
- significant associationse5
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e5“GWAS analysis identified significant associations with a gene encoding a small secreted protein”
Claim · model-written summary
A candidate gene for the previously mapped AvrHar was identified.
- Taxon
- barleyHordeum vulgaree0
- Gene
- AvrHare6
- Outcome
- candidate genee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e6“we identified a candidate gene for the previously mapped AvrHar”
Claim · model-written summary
Disrupting AvrHar in isolate 15A did not change the phenotype.
- Taxon
- barleyHordeum vulgaree0
- Treatment
- Disruption of AvrHare7
- Interactor
- isolate 15Ae7pathogen
- Gene
- AvrHare7
- Outcome
- phenotypic changee7
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e7“Disruption of AvrHar in isolate 15A did not result in a phenotypic change”
Claim · model-written summary
Disrupting the 0-1 allele caused a complete loss of pathogenicity.
- Taxon
- barleyHordeum vulgaree0
- Treatment
- disruption of the 0-1 allelee7
- Outcome
- pathogenicitye7
- Direction
- complete losse7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e7“disruption of the 0-1 allele resulted in a complete loss of pathogenicity”
Claim · model-written summary
The reference isolate 0-1 was sequenced and assembled into 12 chromosomes, giving the first finished genome of P. teres f. teres.
- Taxon
- barleyHordeum vulgaree0
- Material
- reference isolate 0-1e1
- Outcome
- first finished genomee1
- Value
- 12 chromosomese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pyrenophora teres f. teres is the causal agent of net form net blotch of barley”
e1“the reference isolate 0-1 was sequenced and assembled using PacBio single molecule real-time (SMRT) sequencing and scaffolded into 12 chromosomes to provide the first finished genome of P. teres f. teres”
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