Abstract
Background: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. Results: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. Conclusions: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
| Original language | English (US) |
|---|---|
| Article number | 5214 |
| Journal | BMC Genomics |
| Volume | 19 |
| Issue number | 1 |
| DOIs | |
| State | Published - Nov 29 2018 |
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Keywords
- Biotrophy
- Gene loss
- Genomics
- Oomycete
- Peronospora effusa
- Peronospora farinosa
- Peronospora lineage
- Spinach downy mildew
ASJC Scopus subject areas
- Biotechnology
- Genetics
Cite this
Comparative genomics of downy mildews reveals potential adaptations to biotrophy. / Fletcher, Kyle; Klosterman, Steven J.; Derevnina, Lida; Martin, Frank; Bertier, Lien D.; Koike, Steven; Reyes-Chin-Wo, Sebastian; Mou, Beiquan; Michelmore, Richard W.
In: BMC Genomics, Vol. 19, No. 1, 5214, 29.11.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Comparative genomics of downy mildews reveals potential adaptations to biotrophy
AU - Fletcher, Kyle
AU - Klosterman, Steven J.
AU - Derevnina, Lida
AU - Martin, Frank
AU - Bertier, Lien D.
AU - Koike, Steven
AU - Reyes-Chin-Wo, Sebastian
AU - Mou, Beiquan
AU - Michelmore, Richard W
PY - 2018/11/29
Y1 - 2018/11/29
N2 - Background: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. Results: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. Conclusions: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
AB - Background: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. Results: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. Conclusions: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
KW - Biotrophy
KW - Gene loss
KW - Genomics
KW - Oomycete
KW - Peronospora effusa
KW - Peronospora farinosa
KW - Peronospora lineage
KW - Spinach downy mildew
UR - http://www.scopus.com/inward/record.url?scp=85057561860&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85057561860&partnerID=8YFLogxK
U2 - 10.1186/s12864-018-5214-8
DO - 10.1186/s12864-018-5214-8
M3 - Article
C2 - 30486780
AN - SCOPUS:85057561860
VL - 19
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 1
M1 - 5214
ER -