Abstract
Phytophthora cinnamomi is a hemibiotrophic oomycete causing Phytophthora root rot in over 5,000 plant species, threatening natural ecosystems, forestry, and agriculture. Genomic studies of P. cinnamomi are limited compared to other Phytophthora spp. despite the importance of this destructive and highly invasive pathogen. The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing. Genome sizes were estimated by flow cytometry and assembled de novo to 140–141 Mb genomes with 21,111–21,402 gene models. Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model. The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate. Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana , and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors. Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes. Our study also provides insights into common and host-specific P. cinnamomi infection strategies and may serve as a method for narrowing and selecting key candidate effectors for functional studies to determine their contributions to plant resistance or susceptibility.
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Claims 8
Claim · model-written summary
The two P. cinnamomi isolates from avocado orchards were assembled de novo to 140–141 Mb genomes
- Taxon
- avocado
Persea americanae1 - Interactor
- P. cinnamomi
Phytophthora cinnamomie1pathogen - Outcome
- Genome sizese2
- Value
- 140–141 Mbe2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e2“Genome sizes were estimated by flow cytometry and assembled de novo to 140–141 Mb genomes with 21,111–21,402 gene models”
Claim · model-written summary
The two P. cinnamomi genome assemblies contain 21,111–21,402 gene models
- Taxon
- avocadoPersea americanae1
- Interactor
- P. cinnamomiPhytophthora cinnamomie1pathogen
- Outcome
- gene modelse2
- Value
- 21,111–21,402e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e2“Genome sizes were estimated by flow cytometry and assembled de novo to 140–141 Mb genomes with 21,111–21,402 gene models”
Claim · model-written summary
Both P. cinnamomi isolates exhibit complex heterozygous genomes fitting the two-speed genome model
- Taxon
- avocadoPersea americanae1
- Interactor
- P. cinnamomiPhytophthora cinnamomie1pathogen
- Outcome
- complex heterozygous genomese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e3“Genome analyses revealed that both isolates exhibited complex heterozygous genomes fitting the two-speed genome model”
Claim · model-written summary
The more virulent P. cinnamomi isolate has a larger secretome than the less virulent isolate
- Taxon
- avocadoPersea americanae1
- Material
- more virulent isolatee4
- Interactor
- P. cinnamomiPhytophthora cinnamomie1pathogen
- Outcome
- secretomee4
- Direction
- largere4
- Comparator
- less virulent isolatee4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e4“The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate”
Claim · model-written summary
The more virulent P. cinnamomi isolate encodes more RXLR effectors than the less virulent isolate
- Taxon
- avocadoPersea americanae1
- Material
- more virulent isolatee4
- Interactor
- P. cinnamomiPhytophthora cinnamomie1pathogen
- Outcome
- RXLR effectorse4
- Direction
- moree4
- Comparator
- less virulent isolatee4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e4“The more virulent isolate encodes a larger secretome and more RXLR effectors when compared to the less virulent isolate”
Claim · model-written summary
P. cinnamomi deploys common gene repertoires in all infected hosts
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae5 - Interactor
- P. cinnamomiPhytophthora cinnamomie5pathogen
- Outcome
- common gene repertoirese5
- Qualifier
- in all hostse5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana , and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors”
Claim · model-written summary
P. cinnamomi deploys host-specific gene subsets, especially among effectors
- Taxon
- Arabidopsis thalianaArabidopsis thalianae5
- Interactor
- P. cinnamomiPhytophthora cinnamomie5pathogen
- Outcome
- host-specific subsetse5
- Qualifier
- especially among effectorse5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e5“Transcriptome analysis after P. cinnamomi infection in Arabidopsis thaliana, Nicotiana benthamiana , and Persea americana de Mill (avocado) showed that this pathogen deploys common gene repertoires in all hosts and host-specific subsets, especially among effectors”
Claim · model-written summary
Clonal P. cinnamomi isolates increase phenotypic diversity through polyploidization, gene duplications and a bipartite genome architecture, as other Phytophthora spp. do
- Taxon
- avocadoPersea americanae1
- Interactor
- P. cinnamomiPhytophthora cinnamomie6pathogen
- Outcome
- phenotypic diversitye6
- Qualifier
- polyploidization, gene duplications, and a bipartite genome architecturee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“The genome of two genetically and phenotypically distinct P. cinnamomi isolates collected from avocado orchards in California were sequenced using PacBio and Illumina sequencing”
e6“Overall, our results suggested that clonal P. cinnamomi isolates employ similar strategies as other Phytophthora spp. to increase phenotypic diversity (e.g., polyploidization, gene duplications, and a bipartite genome architecture) to cope with environmental changes”