Author Correction: The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides.
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ABSTRACT:
SUBMITTER: Yang M
PROVIDER: S-EPMC7193557 | biostudies-literature | 2020 May
REPOSITORIES: biostudies-literature
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Author Correction: The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides.
Yang Min M Duan Shengchang S Mei Xinyue X Huang Huichuan H Chen Wei W Liu Yixiang Y Guo Cunwu C Yang Ting T Wei Wei W Liu Xili X He Xiahong X Dong Yang Y Zhu Shusheng S
Scientific reports 20200501 1
An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...[more]
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Project description:Phytophthora cactorum is a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5?Mb genome assembly of the P. cactorum using the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in the Phytophthora genera, which contains 27,981 protein-coding genes. Comparison with other Phytophthora genomes showed that P. cactorum had a closer relationship with P. parasitica, P. infestans and P. capsici. P. cactorum has similar gene families in the secondary metabolism and pathogenicity-related effector proteins compared with other oomycete species, but specific gene families associated with detoxification enzymes and carbohydrate-active enzymes (CAZymes) underwent expansion in P. cactorum. P. cactorum had a higher utilization and detoxification ability against ginsenosides-a group of defense compounds from Panax notoginseng-compared with the narrow host pathogen P. sojae. The elevated expression levels of detoxification enzymes and hydrolase activity-associated genes after exposure to ginsenosides further supported that the high detoxification and utilization ability of P. cactorum play a crucial role in the rapid adaptability of the pathogen to host plant defense compounds and fungicides.
| S-EPMC5916904 | biostudies-literature
Project description:BACKGROUND: Phytophthora cactorum, a hemibiotrophic oomycete pathogen, can cause destructive diseases on numerous crops worldwide, leading to essential economic losses every year. However, little has been known about its molecular pathogenicity mechanisms. To gain insight into its repertoire of effectors, the P. cactorum transcriptome was investigated using Illumina RNA-seq. RESULTS: We first demonstrated an in vitro inoculation method that can be used to mimic natural cyst germination on host plants. Over 28 million cDNA reads were obtained for five life cycle stages (mycelium, sporangium, zoospore, cyst and germinating cyst) and de novo assembled into 21,662 unique genes. By comparisons with 11 public databases, 88.99% of the unique genes were annotated, including 15,845 mapped to the gene models of the annotated relative Phytophthora infestans. Using TribeMCL, 5,538 gene families conserved across P. cactorum and other three completely sequenced Phytophthora pathogen species were determined. In silico analyses revealed that 620 P. cactorum effector homologues including 94 RXLR effector candidates matched known or putative virulence genes in other oomycetes. About half of the RXLR effector candidates were predicted to share a conserved structure unit, termed the WY-domain fold. A subset of the effector genes were checked and validated by PCR amplification. Transcriptional experiments indicated that effector genes were differentially expressed during the life cycle and host infection stages of P. cactorum. Ectopic expression in Nicotiana benthamiana revealed that RXLR, elicitin and NLP effectors can trigger plant cell death. These effectors are highly conserved across oomycete species. Single nucleotide polymorphisms for RXLR effectors were detected in a collection of P. cactorum isolates from different countries and hosts. CONCLUSIONS: This study demonstrates the comprehensive sequencing, de novo assembly, and analyses of the transcriptome of P. cactorum life cycle stages. In the absence of genome sequence, transcriptome data is important for infection-related gene discovery in P. cactorum, as demonstrated here for the effector genes. The first look at the transcriptome and effector arsenal of P. cactorum provides valuable data to elucidate the pathogenicity basis of this broad-host-range pathogen.
| S-EPMC4289400 | biostudies-literature
Project description:An amendment to this paper has been published and can be accessed via a link at the top of the paper.
| S-EPMC7962561 | biostudies-literature
Project description:[This corrects the article DOI: 10.1038/s41438-018-0108-0.].
| S-EPMC6474867 | biostudies-literature
Project description:Phytophthora cactorum Genome sequencing and assembly
| PRJNA318145 | ENA
Project description: Not available
| S-EPMC8100179 | biostudies-literature
Project description:Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.
| S-EPMC8285097 | biostudies-literature
Project description:Farnesol, geranylgeraniol, dolichols and ubiquinones were the main radioactive components of the unsaponifiable lipid recovered from Phytophthora cactorum grown in aerated cultures containing [2-(14)C]mevalonate. The (14)C recovered in each of these components was in the approximate proportion 2:4:3:5. When the culture was not aerated no radioactive ubiquinone was recovered. Most of the (14)C recovered in the dolichols was found in dolichol-15 (37%), with decreasing amounts in dolichol-14 (30%) and -13 (14%) and only a little (5%) in dolichol-16, whereas the major components, by weight, of the mixture (13mug/g of damp-dry tissue) were dolichol-14, -15 and -16 in the approximate proportion of 1:3:1. Radioautography of appropriate chromatograms indicated the presence also of traces of radioactivity in dolichol-9, -10, -11, -12 and -17. Most (80%) of the (14)C recovered in the ubiquinones was associated with ubiquinone-9, the rest being in ubiquinone-8. Most (80%) of the weight of ubiquinones (19mug/g of damp-dry tissue) was also ubiquinone-9. The identification of these compounds was by chromatographic methods and, for the ubiquinones and dolichols, was confirmed by mass spectrometry. In addition, the incorporation of 4R- and/or 4S-(3)H from [4-(3)H]-mevalonates showed the expected stereochemistry of biosynthesis, namely that farnesol, geranylgeraniol and ubiquinones were biogenetically all trans and the dolichols each contained three biogenetically trans isoprene residues, the remaining residues being biogenetically cis. The distribution of (14)C in the components of the whole lipid of the fungus was consistent with 97% of both the farnesol and geranylgeraniol being present as the fatty acid ester. The corresponding value for dolichols was 37%. The observation by other workers, that this fungus does not form either squalene or sterol, was confirmed.
| S-EPMC1174023 | biostudies-other
Project description:Crown rot (Phytophthora cactorum) causes significant economic losses in strawberry production. The best control strategy would be to use resistant cultivars, but polygenically inherited resistance makes the breeding of the garden strawberry (Fragaria × ananassa) challenging. The diploid wild strawberry Fragaria vesca Hawaii 4 genotype was shown previously to have resistance against crown rot. To explore the resistance mechanisms, we inoculated the roots of Hawaii 4 with P. cactorum in a novel in vitro hydroponic system to minimize interference caused by other microbes. Major reprogramming of the root transcriptome occurred, involving 30% of the genes. The surveillance system of the plant shifted from the development mode to the defense mode. Furthermore, the immune responses as well as many genes involved in the biosynthesis of the defense hormones jasmonic acid, ethylene and salicylic acid were up-regulated. Several major allergen-like genes encoding PR-10 proteins were highly expressed in the inoculated plants, suggesting that they also have a crucial role in the defense responses against P. cactorum. Additionally, flavonoids and terpenoids may be of vital importance, as several genes involved in their biosynthesis were up-regulated. The cell wall biosynthesis and developmental processes were down-regulated, possibly as a result of the down-regulation of the key genes involved in the biosynthesis of growth-promoting hormones brassinosteroids and auxin. Of particular interest was the expression of potential resistance genes in the recently identified P. cactorum resistance locus RPc-1. These new findings help to target the breeding efforts aiming at more resistant strawberry cultivars.
| S-EPMC4982697 | biostudies-literature