Whole Genome Sequences of the Raspberry and Strawberry Pathogens <i>Phytophthora rubi</i> and <i>P. fragariae</i>

Tabima, Javier F.; Kronmiller, Brent; Press, Caroline M.; Tyler, Brett M.; Zasada, Inga A.; Grünwald, Niklaus J.

doi:10.1094/mpmi-04-17-0081-a

Cited by 15 publications

(9 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This study produced assemblies of an additional ten isolates of P. fragariae and three isolates of the closely related raspberry pathogen P. rubi with short read technology. These assemblies were of similar sizes and contiguity to those previously published (Gao et al, 2015;Tabima et al, 2017).…”

Section: Discussionsupporting

confidence: 76%

“…This study utilised long read sequencing technologies to improve the contiguity of the P. fragariae genome through the assembly of a greater amount of repeat rich sequence. Though this assembly still fell short of the estimated chromosome number of 10 -12 (Brasier et al, 1999), at 180 contigs, it is a significant improvement over the previous assemblies that utilised solely short read technologies and produced relatively fragmented assemblies, comprised of >1,000 contigs each (Gao et al, 2015;Tabima et al, 2017). The increase in size of the assembly presented (91 Mb), suggests that the assembly includes an increased amount of repetitive sequence, indicating that it represents a more complete genome assembly than previous attempts.…”

Section: Discussionmentioning

confidence: 95%

“…All publicly available genome assemblies of P. fragariae have to date solely utilised Illumina short read sequencing technologies, resulting in assemblies of 73.68 and 76 Mb, in 1,616 and 8,511 scaffolds, respectively (Gao et al, 2015;Tabima et al, 2017). Recently, long read sequencing technology has been shown to provide assemblies of improved contiguity for P. pathogens, specifically the generation of the haplotype-phased assembly of P. ramorum (60.5 Mb in 302 primary contigs) using PacBio sequencing (Malar et al, 2019) and the assembly of P. capsici (95.2 Mb in 424 scaffolds) using Oxford Nanopore Technology (Cui et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

et al. 2020

Self Cite

View full text Add to dashboard Cite

The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, "red core". The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens.

show abstract

Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…P. cinnamomi also has all five tandem homologs in the same orientation, but in a different order than P. sojae : AGO 4, AGO 5, AGO 8, AGO 9, and AGO 3. P. fragariae and P. rubi ( Tabima et al, 2017 ) have three of the five clustered homologs ( AGO 4, AGO 3, AGO 9) in the same orientation, but different orders, and only AGO 3 of the tandem set was identified in P. niederhauserii ; however, we cannot rule out the possibility that sequences were missed in the genome assembly. Only two other genes grouped within the AGO5/8/9 group of homologs, specifically the AGO5 group, but these genes were not physically as close to the AGO 4 and AGO 3 genes as in clade 7 species.…”

Section: Resultsmentioning

confidence: 99%

Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora

et al. 2018

Self Cite

View full text Add to dashboard Cite

Modulation of gene expression through RNA interference is well conserved in eukaryotes and is involved in many cellular processes. In the oomycete Phytophthora, research on the small RNA machinery and function has started to reveal potential roles in the pathogen, but much is still unknown. We examined Argonaute (AGO) homologs within oomycete genome sequences, especially among Phytophthora species, to gain a clearer understanding of the evolution of this well-conserved protein family. We identified AGO homologs across many representative oomycete and stramenopile species, and annotated representative homologs in P. sojae. Furthermore, we demonstrate variable transcript levels of all identified AGO homologs in comparison to previously identified Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) homologs. Our phylogenetic analysis further refines the relationship of the AGO homologs in oomycetes and identifies a conserved tandem duplication of AGO homologs in a subset of Phytophthora species.

show abstract

“…Both of the abovementioned studies utilized a shot-gun approach, and the application of the Illumina platform was utilized for P. rubi and P. fragariae . The pathogen genetic material sequencing resulted in a 76-fold coverage of 5.88 Mb for P. fragariae and a 92-fold coverage of 6.96 Mb for P. rubi [122].…”

Section: Detection Methods Of Plant Pathogenic Fungal Speciesmentioning

confidence: 99%

Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops—A Review

2019

View full text Add to dashboard Cite

Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.

show abstract

Whole Genome Sequences of the Raspberry and Strawberry Pathogens Phytophthora rubi and P. fragariae

Cited by 15 publications

References 9 publications

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races

Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora

Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops—A Review

Contact Info

Product

Resources

About