Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus

Gao, Ruifang; Yinghui, Cheng; Wang, Ying; Guo, Liyun; Zhang, Guiming

doi:10.1128/genomea.00034-15

Cited by 17 publications

(4 citation statements)

References 8 publications

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“…The lengths of 97.3% scaffolds were greater than 5 Kb (Table 1 ). The genome of P. cactorum is the second largest among the sequenced Phytophthora species, only smaller than P. infestans (~240 Mb) 19 , but larger than P. lateralis (~44 Mb) 20 , P. capsici (~64 Mb) 21 , P. ramorum (~65 Mb) 22 , P. fragariae (~73.68 Mb) 23 , P. parasitica (~64.5 Mb) 24 , and P. sojae (~95 Mb) 22 . Based on the protists dataset in BUSCO 25 , the genome captured 170 (79.1%) complete BUSCOs (Benchmarking Universal Single-Copy Orthologs).…”

Section: Resultsmentioning

confidence: 99%

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

Yang

Duan

Mei

et al. 2018

Sci Rep

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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.

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Section: Resultsmentioning

confidence: 99%

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

Yang

Duan

Mei

et al. 2018

Sci Rep

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“…According to our K -mer analysis, the estimated actual genome sizes of P. fragariae 309.62 and P. rubi 109892 are 91.2 Mb and 103.4 Mb, respectively (Figure S1). The size of the final assembly of the P. fragariae genome is 75.98 Mb, with an 84.00 kb scaffold N50 and corresponding 40.50 kb contig N50 ( Gao et al., 2015 ). The P. rubi genome assembly is 79.10 Mb, with an 83.99 kb scaffold N50 and corresponding 13.67 kb contig N50 (Tables S1 and S2).…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

Gao

Wang

Liu

et al. 2021

Heliyon

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The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species– P. fragariae and P. rubi . Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies.

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“…In the past decades, genomes of multiple species of Phytophthora , such as P. infestans ( Haas et al., 2009 ), P. sojae , P. ramorum ( Tyler et al., 2006 ), P. capsici ( Lamour et al., 2012 ), and P. fragariae ( Gao et al., 2015 ) were sequenced. Recently, a draft genome of one isolate of P. rubi of raspberry was reported from the western USA ( Tabima et al., 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Genome resources and whole genome resequencing of Phytophthora rubi isolates from red raspberry

et al. 2023

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Phytophthora rubi is a primary causal agent of Phytophthora root rot and wilting of raspberry (Rubus idaeus L.) worldwide. The disease is a major concern for raspberry growers in Canada and USA. To date, no information is available on genomic diversity of P. rubi population from raspberry in Canada. Using a PCR-free library prep with dual-indexing for an Illumina HiSEQX running a 2x150 bp configuration, we generated whole genome sequence data of P. rubi isolates (n = 25) recovered during 2018 to 2020 from nine fields, four locations and four cultivars of raspberry growing areas of British Columbia, Canada. The assembled genome of 24 isolates of P. rubi averaged 8,541 scaffolds, 309× coverage, and 65,960,000 bp. We exploited single nucleotide polymorphisms (SNPs) obtained from whole genome sequence data to analyze the genome structure and genetic diversity of the P. rubi isolates. Low heterozygosity among the 72% of pathogen isolates and standardized index of association revealed that those isolates were clonal. Principal component analysis, discriminant analysis of principal component, and phylogenetic tree revealed that P. rubi isolates clustered with the raspberry specific cultivars. This study provides novel resources and insight into genome structure, genetic diversity, and reproductive biology of P rubi isolated from red raspberry. The availability of the P. rubi genomes also provides valuable resources for future comparative genomic and evolutionary studies for oomycetes pathogens.

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Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus

Cited by 17 publications

References 8 publications

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

Genome resources and whole genome resequencing of Phytophthora rubi isolates from red raspberry

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