The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

M. Thines, R. Sharma, Y.A. Rodenburg, A. Gogleva, H.S. Judelson, X. Xia, D.J. van den Hoogen, M. Kitner, J. Klein, M. Neilen, D. de Ridder, M.F. Seidl, G. van den Ackerveken, F. Govers, S. Schornack, D.J. Studholme

Research output: Working paperAcademic

Abstract

Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
Original languageEnglish
PublisherBioRxiv
DOIs
Publication statusPublished - 31 Jul 2019

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Peronospora
heterozygosity
Oomycetes
promoter regions
genome
Plasmopara
microsatellite repeats
basil
repetitive sequences
convergent evolution
pathogens
downy mildew
host specificity
nuclear genome
lifestyle
population genetics
virulence
genomics
seeds
genes

Cite this

Thines, M. ; Sharma, R. ; Rodenburg, Y.A. ; Gogleva, A. ; Judelson, H.S. ; Xia, X. ; van den Hoogen, D.J. ; Kitner, M. ; Klein, J. ; Neilen, M. ; de Ridder, D. ; Seidl, M.F. ; van den Ackerveken, G. ; Govers, F. ; Schornack, S. ; Studholme, D.J. / The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters. BioRxiv, 2019.
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abstract = "Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 {\%} of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.",
author = "M. Thines and R. Sharma and Y.A. Rodenburg and A. Gogleva and H.S. Judelson and X. Xia and {van den Hoogen}, D.J. and M. Kitner and J. Klein and M. Neilen and {de Ridder}, D. and M.F. Seidl and {van den Ackerveken}, G. and F. Govers and S. Schornack and D.J. Studholme",
year = "2019",
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doi = "10.1101/721027",
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Thines, M, Sharma, R, Rodenburg, YA, Gogleva, A, Judelson, HS, Xia, X, van den Hoogen, DJ, Kitner, M, Klein, J, Neilen, M, de Ridder, D, Seidl, MF, van den Ackerveken, G, Govers, F, Schornack, S & Studholme, DJ 2019 'The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters' BioRxiv. https://doi.org/10.1101/721027

The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters. / Thines, M.; Sharma, R.; Rodenburg, Y.A.; Gogleva, A.; Judelson, H.S.; Xia, X.; van den Hoogen, D.J.; Kitner, M.; Klein, J.; Neilen, M.; de Ridder, D.; Seidl, M.F.; van den Ackerveken, G.; Govers, F.; Schornack, S.; Studholme, D.J.

BioRxiv, 2019.

Research output: Working paperAcademic

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T1 - The genome of Peronospora belbahrii reveals high heterozygosity, a low number of canonical effectors and CT-rich promoters

AU - Thines, M.

AU - Sharma, R.

AU - Rodenburg, Y.A.

AU - Gogleva, A.

AU - Judelson, H.S.

AU - Xia, X.

AU - van den Hoogen, D.J.

AU - Kitner, M.

AU - Klein, J.

AU - Neilen, M.

AU - de Ridder, D.

AU - Seidl, M.F.

AU - van den Ackerveken, G.

AU - Govers, F.

AU - Schornack, S.

AU - Studholme, D.J.

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N2 - Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.

AB - Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was ca. 35.4 Mbp in length, with an N50 scaffold length of ca. 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of ca. 40.1 kbp. From the repeat-masked genome 9049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16 % of the genome consists of repetitive sequences, and based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of Pe. belbahrii. Peronospora belbahrii has undergone a high degree of convergent evolution, reflecting its obligate biotrophic lifestyle. Features of its secretome, signalling networks, and promoters are presented, and some patterns are hypothesised to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.

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