Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina
Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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The American Phytopathological Society
2015-11-01
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| Series: | Molecular Plant-Microbe Interactions |
| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/MPMI-05-15-0112-R |
| _version_ | 1828231212561334272 |
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| author | Lida Derevnina Sebastian Chin-Wo-Reyes Frank Martin Kelsey Wood Lutz Froenicke Otmar Spring Richard Michelmore |
| author_facet | Lida Derevnina Sebastian Chin-Wo-Reyes Frank Martin Kelsey Wood Lutz Froenicke Otmar Spring Richard Michelmore |
| author_sort | Lida Derevnina |
| collection | DOAJ |
| description | Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain–containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens. |
| first_indexed | 2024-04-12T19:00:17Z |
| format | Article |
| id | doaj.art-e8d9aa7820ce49e692cce884bfeb690d |
| institution | Directory Open Access Journal |
| issn | 0894-0282 1943-7706 |
| language | English |
| last_indexed | 2024-04-12T19:00:17Z |
| publishDate | 2015-11-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Molecular Plant-Microbe Interactions |
| spelling | doaj.art-e8d9aa7820ce49e692cce884bfeb690d2022-12-22T03:20:12ZengThe American Phytopathological SocietyMolecular Plant-Microbe Interactions0894-02821943-77062015-11-0128111198121510.1094/MPMI-05-15-0112-RGenome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacinaLida Derevnina0Sebastian Chin-Wo-Reyes1Frank Martin2Kelsey Wood3Lutz Froenicke4Otmar Spring5Richard Michelmore6Genome Center, University of California Davis, Davis, CA, U.S.A.;Genome Center, University of California Davis, Davis, CA, U.S.A.;United States Department of Agriculture-Agricultural Research Service, Salinas, CA U.S.A.;Genome Center, University of California Davis, Davis, CA, U.S.A.;Genome Center, University of California Davis, Davis, CA, U.S.A.;Institute of Botany, University of Hohenheim, GermanyGenome Center, University of California Davis, Davis, CA, U.S.A.;Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain–containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.https://apsjournals.apsnet.org/doi/10.1094/MPMI-05-15-0112-R |
| spellingShingle | Lida Derevnina Sebastian Chin-Wo-Reyes Frank Martin Kelsey Wood Lutz Froenicke Otmar Spring Richard Michelmore Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina Molecular Plant-Microbe Interactions |
| title | Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina |
| title_full | Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina |
| title_fullStr | Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina |
| title_full_unstemmed | Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina |
| title_short | Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina |
| title_sort | genome sequence and architecture of the tobacco downy mildew pathogen peronospora tabacina |
| url | https://apsjournals.apsnet.org/doi/10.1094/MPMI-05-15-0112-R |
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