Genome sequences of six Phytophthora species associated with forests in New Zealand

Studholme, David J.; McDougal, Rebecca; Sambles, Christine; Hansen, E. M.; Hardy, G.; Grant, Murray; Ganley, Rebecca J.; Williams, N.

doi:10.1016/j.gdata.2015.11.015

Cited by 54 publications

(70 citation statements)

References 11 publications

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“…Annotated genome assemblies and raw sequence data are available via GenBank (Table ). The assembly statistics for the genome sequences presented are comparable with those published previously (Feau et al , ; Sambles et al , ; Studholme et al , ), with the exception of Chile 5. This genome assembly had a larger number of scaffolds and appeared to be much larger in total length (Table ).…”

Section: Isolates Used In This Study and Summary Statistics For Genomsupporting

confidence: 85%

“…Genomes have been sequenced for isolates of P. kernoviae from New Zealand (Studholme et al , ) and the UK (Feau et al , ; Sambles et al , ). Here, we report the first genome sequences for isolates of P. kernoviae from Chile (Table ), the only other geographical location in which this species has been reported so far.…”

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

“…Completeness for genes from Chile 1, Chile 2, Chile 4, Chile 6 and Chile 7 (95.7%–97.9%) was similar to that of recently published P . kernoviae genomes (97.4%–97.9%) (Feau et al , ; Sambles et al , ; Studholme et al , ) (Table ). The Chile 5 assembly was less complete (87.6%) and had a considerably higher number of duplicated genes (164) compared with the other genomes, which had less than four duplicated genes.…”

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

“…Sequencing reads from the six Chilean genomes were aligned with those of the other available P . kernoviae isolates from the UK and New Zealand (Sambles et al , ; Studholme et al , ). Chile 1, Chile 2 and Chile 4 clustered adjacent to the P. kernoviae isolates from New Zealand and the UK (Fig.…”

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

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Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

Studholme

Panda

Sanfuentes

et al. 2018

Molecular Plant Pathology

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Summary Genome sequences were generated for six oomycete isolates collected from forests in Valdivia, Chile. Three of the isolates were identified morphologically as Phytophthora kernoviae , whereas two were similar to other clade 10 Phytophthora species. One isolate was tentatively identified as Nothophytophthora valdiviana based on nucleotide sequence similarity in the cytochrome oxidase 1 gene. This is the first genome sequence for this recently described genus. The genome assembly was more fragmented and contained many duplicated genes when compared with the other Phytophthora sequences. Comparative analyses were performed with genomic sequences of the P. kernoviae isolates from the UK and New Zealand. Although the potential New Zealand origin of P. kernoviae has been suggested, new isolations from Chile had cast doubt on this hypothesis. We present evidence supporting P. kernoviae as having originated in New Zealand. However, investigation of the diversity of oomycete species in Chile has been limited and warrants further exploration. We demonstrate the expediency of genomic analyses in determining phylogenetic relationships between isolates within new and often scantly represented taxonomic groups, such as Phytophthora clade 10 and Nothophytophthora . Data are available on GenBank via BioProject accession number PRJNA352331.

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Section: Isolates Used In This Study and Summary Statistics For Genomsupporting

confidence: 85%

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

Section: Isolates Used In This Study and Summary Statistics For Genommentioning

confidence: 99%

See 2 more Smart Citations

Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

Studholme

Panda

Sanfuentes

et al. 2018

Molecular Plant Pathology

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“…See Studholme et al . (2015) 1 . So, the authors' assertion (in their Conclusions section) that this is the first genome assembly from an Australian strain should be revised.…”

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confidence: 99%

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

2017

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Background: The oomycete plant pathogen, Phytophthora cinnamomi, is responsible for the destruction of thousands of species of native Australian plants, as well as several crops, such as avocado and macadamia, and has one of the widest host-plant ranges of the Phytophthora genus. The currently available genome of P. cinnamomi is based on an atypical strain and has large gaps in its assembly. To further studies of the pathogenicity of this species, especially in Australia, more robust assemblies of the genomes of more typical strains are required. Here we report the genome sequencing, draft assembly, and preliminary annotation of two geographically separated Australian strains of P. cinnamomi. Findings: Some 308 million raw reads were generated for the two strains. Independent genome assembly produced final genomes of 62.8 Mb (in 14,268 scaffolds) and 68.1 Mb (in 10,084 scaffolds), which are comparable in size and contiguity to other Phytophthora genomes. Gene prediction yielded > 22,000 predicted protein-encoding genes within each genome, while BUSCO assessment showed 82.5% and 81.8% of the eukaryote universal single-copy orthologs to be present in the assembled genomes, respectively. Conclusions: The assembled genomes of two geographically distant isolates of Phytophthora cinnamomi will provide a valuable resource for further comparative analysis and evolutionary studies of this destructive pathogen, and further annotation of the presented genomes may yield possible targets for novel pathogen control methods.

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Genome projects in invasion biology

2019

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Genome sequences of six Phytophthora species associated with forests in New Zealand

Cited by 54 publications

References 11 publications

Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi

Genome projects in invasion biology

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