Comparative genomics of downy mildews reveals potential adaptations to biotrophy.
Identifieur interne : 000820 ( Main/Exploration ); précédent : 000819; suivant : 000821Comparative genomics of downy mildews reveals potential adaptations to biotrophy.
Auteurs : Kyle Fletcher [États-Unis] ; Steven J. Klosterman [États-Unis] ; Lida Derevnina [États-Unis, Royaume-Uni] ; Frank Martin [États-Unis] ; Lien D. Bertier [États-Unis] ; Steven Koike [États-Unis] ; Sebastian Reyes-Chin-Wo [États-Unis] ; Beiquan Mou [États-Unis] ; Richard Michelmore [États-Unis]Source :
- BMC genomics [ 1471-2164 ] ; 2018.
Descripteurs français
- KwdFr :
- Adaptation physiologique (génétique), Analyse de séquence d'ARN (MeSH), Annotation de séquence moléculaire (MeSH), Fonctions de vraisemblance (MeSH), Génomique (MeSH), Hétérozygote (MeSH), Maladies des plantes (microbiologie), Mitochondries (génétique), Peronospora (génétique), Peronospora (pathogénicité), Phylogenèse (MeSH), Séquences répétées terminales (génétique).
- MESH :
- génétique : Adaptation physiologique, Mitochondries, Peronospora, Séquences répétées terminales.
- microbiologie : Maladies des plantes.
- pathogénicité : Peronospora.
- Analyse de séquence d'ARN, Annotation de séquence moléculaire, Fonctions de vraisemblance, Génomique, Hétérozygote, Phylogenèse.
English descriptors
- KwdEn :
- Adaptation, Physiological (genetics), Genomics (MeSH), Heterozygote (MeSH), Likelihood Functions (MeSH), Mitochondria (genetics), Molecular Sequence Annotation (MeSH), Peronospora (genetics), Peronospora (pathogenicity), Phylogeny (MeSH), Plant Diseases (microbiology), Sequence Analysis, RNA (MeSH), Terminal Repeat Sequences (genetics).
- MESH :
- genetics : Adaptation, Physiological, Mitochondria, Peronospora, Terminal Repeat Sequences.
- microbiology : Plant Diseases.
- pathogenicity : Peronospora.
- Genomics, Heterozygote, Likelihood Functions, Molecular Sequence Annotation, Phylogeny, Sequence Analysis, RNA.
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 N
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.
DOI: 10.1186/s12864-018-5214-8
PubMed: 30486780
PubMed Central: PMC6264045
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Klosterman, Steven J" sort="Klosterman, Steven J" uniqKey="Klosterman S" first="Steven J" last="Klosterman">Steven J. Klosterman</name><affiliation wicri:level="1"><nlm:affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905</wicri:regionArea><wicri:noRegion>93905</wicri:noRegion></affiliation></author><author><name sortKey="Derevnina, Lida" sort="Derevnina, Lida" uniqKey="Derevnina L" first="Lida" last="Derevnina">Lida Derevnina</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH</wicri:regionArea><wicri:noRegion>NR4 7UH</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Frank" sort="Martin, Frank" uniqKey="Martin F" first="Frank" last="Martin">Frank Martin</name><affiliation wicri:level="1"><nlm:affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905</wicri:regionArea><wicri:noRegion>93905</wicri:noRegion></affiliation></author><author><name sortKey="Bertier, Lien D" sort="Bertier, Lien D" uniqKey="Bertier L" first="Lien D" last="Bertier">Lien D. Bertier</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Koike, Steven" sort="Koike, Steven" uniqKey="Koike S" first="Steven" last="Koike">Steven Koike</name><affiliation wicri:level="1"><nlm:affiliation>UC Davis Cooperative Extension Monterey County, Salinas, CA, 93901, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>UC Davis Cooperative Extension Monterey County, Salinas, CA, 93901</wicri:regionArea><wicri:noRegion>93901</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Present Address: TriCal Diagnostics, Hollister, CA, 95023, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Present Address: TriCal Diagnostics, Hollister, CA, 95023</wicri:regionArea><wicri:noRegion>95023</wicri:noRegion></affiliation></author><author><name sortKey="Reyes Chin Wo, Sebastian" sort="Reyes Chin Wo, Sebastian" uniqKey="Reyes Chin Wo S" first="Sebastian" last="Reyes-Chin-Wo">Sebastian Reyes-Chin-Wo</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author><author><name sortKey="Mou, Beiquan" sort="Mou, Beiquan" uniqKey="Mou B" first="Beiquan" last="Mou">Beiquan Mou</name><affiliation wicri:level="1"><nlm:affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905</wicri:regionArea><wicri:noRegion>93905</wicri:noRegion></affiliation></author><author><name sortKey="Michelmore, Richard" sort="Michelmore, Richard" uniqKey="Michelmore R" first="Richard" last="Michelmore">Richard Michelmore</name><affiliation wicri:level="1"><nlm:affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA. rwmichelmore@ucdavis.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616, USA. rwmichelmore@ucdavis.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (genetics)</term><term>Genomics (MeSH)</term><term>Heterozygote (MeSH)</term><term>Likelihood Functions (MeSH)</term><term>Mitochondria (genetics)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Peronospora (genetics)</term><term>Peronospora (pathogenicity)</term><term>Phylogeny (MeSH)</term><term>Plant Diseases (microbiology)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Terminal Repeat Sequences (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation physiologique (génétique)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Fonctions de vraisemblance (MeSH)</term><term>Génomique (MeSH)</term><term>Hétérozygote (MeSH)</term><term>Maladies des plantes (microbiologie)</term><term>Mitochondries (génétique)</term><term>Peronospora (génétique)</term><term>Peronospora (pathogénicité)</term><term>Phylogenèse (MeSH)</term><term>Séquences répétées terminales (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Adaptation, Physiological</term><term>Mitochondria</term><term>Peronospora</term><term>Terminal Repeat Sequences</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Adaptation physiologique</term><term>Mitochondries</term><term>Peronospora</term><term>Séquences répétées terminales</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Peronospora</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Peronospora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genomics</term><term>Heterozygote</term><term>Likelihood Functions</term><term>Molecular Sequence Annotation</term><term>Phylogeny</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Annotation de séquence moléculaire</term><term>Fonctions de vraisemblance</term><term>Génomique</term><term>Hétérozygote</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>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.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>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 N</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>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.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30486780</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>21</Day></DateCompleted><DateRevised><Year>2019</Year><Month>03</Month><Day>21</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>Nov</Month><Day>29</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of downy mildews reveals potential adaptations to biotrophy.</ArticleTitle><Pagination><MedlinePgn>851</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-018-5214-8</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="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 N<sub>50</sub>s (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.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fletcher</LastName><ForeName>Kyle</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Klosterman</LastName><ForeName>Steven J</ForeName><Initials>SJ</Initials><AffiliationInfo><Affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Derevnina</LastName><ForeName>Lida</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Frank</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bertier</LastName><ForeName>Lien D</ForeName><Initials>LD</Initials><AffiliationInfo><Affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koike</LastName><ForeName>Steven</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>UC Davis Cooperative Extension Monterey County, Salinas, CA, 93901, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Present Address: TriCal Diagnostics, Hollister, CA, 95023, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reyes-Chin-Wo</LastName><ForeName>Sebastian</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mou</LastName><ForeName>Beiquan</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>United States Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Michelmore</LastName><ForeName>Richard</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA. rwmichelmore@ucdavis.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616, USA. rwmichelmore@ucdavis.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P30 CA093373</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>S10 OD018223</GrantID><Acronym>OD</Acronym><Agency>NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>S10 RR026825</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>Endowed Chair in Genomics</GrantID><Agency>Novozymes Inc.</Agency><Country></Country></Grant><Grant><GrantID>C06 RR012088</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United 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