Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics.
Identifieur interne : 000B34 ( Main/Exploration ); précédent : 000B33; suivant : 000B35Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics.
Auteurs : Wenwu Ye [République populaire de Chine] ; Yang Wang [République populaire de Chine] ; Danyu Shen [République populaire de Chine] ; Delong Li [République populaire de Chine] ; Tianhuizi Pu [République populaire de Chine] ; Zide Jiang [République populaire de Chine] ; Zhengguang Zhang [République populaire de Chine] ; Xiaobo Zheng [République populaire de Chine] ; Brett M. Tyler [États-Unis] ; Yuanchao Wang [République populaire de Chine]Source :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2016.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Données de séquences moléculaires (MeSH), Fruit (parasitologie), Génomique (MeSH), Litchi (parasitologie), Maladies des plantes (parasitologie), Phylogenèse (MeSH), Phytophthora (classification), Phytophthora (génétique), Phytophthora (physiologie), Structure tertiaire des protéines (MeSH), Séquence nucléotidique (MeSH).
- MESH :
- génétique : Phytophthora.
- parasitologie : Fruit, Litchi, Maladies des plantes.
- physiologie : Phytophthora.
- classification : Analyse de séquence d'ADN, Données de séquences moléculaires, Génomique, Phylogenèse, Phytophthora, Structure tertiaire des protéines, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Fruit (parasitology), Genomics (MeSH), Litchi (parasitology), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Phytophthora (classification), Phytophthora (genetics), Phytophthora (physiology), Plant Diseases (parasitology), Protein Structure, Tertiary (MeSH), Sequence Analysis, DNA (MeSH).
- MESH :
- classification : Phytophthora.
- genetics : Phytophthora.
- parasitology : Fruit, Litchi, Plant Diseases.
- physiology : Phytophthora.
- Base Sequence, Genomics, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Sequence Analysis, DNA.
Abstract
On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.
DOI: 10.1094/MPMI-03-16-0056-R
PubMed: 27183038
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yang" sort="Wang, Yang" uniqKey="Wang Y" first="Yang" last="Wang">Yang Wang</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Shen, Danyu" sort="Shen, Danyu" uniqKey="Shen D" first="Danyu" last="Shen">Danyu Shen</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Li, Delong" sort="Li, Delong" uniqKey="Li D" first="Delong" last="Li">Delong Li</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Pu, Tianhuizi" sort="Pu, Tianhuizi" uniqKey="Pu T" first="Tianhuizi" last="Pu">Tianhuizi Pu</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Zide" sort="Jiang, Zide" uniqKey="Jiang Z" first="Zide" last="Jiang">Zide Jiang</name><affiliation wicri:level="1"><nlm:affiliation>3 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>3 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642</wicri:regionArea><placeName><settlement type="city">Jiangmen</settlement><region type="province">Guangdong</region></placeName></affiliation></author><author><name sortKey="Zhang, Zhengguang" sort="Zhang, Zhengguang" uniqKey="Zhang Z" first="Zhengguang" last="Zhang">Zhengguang Zhang</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Zheng, Xiaobo" sort="Zheng, Xiaobo" uniqKey="Zheng X" first="Xiaobo" last="Zheng">Xiaobo Zheng</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author><author><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name><affiliation wicri:level="2"><nlm:affiliation>2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.; and.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">États-Unis</country><wicri:regionArea>2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea><wicri:noRegion>Nanjing 210095</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Fruit (parasitology)</term><term>Genomics (MeSH)</term><term>Litchi (parasitology)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Phytophthora (classification)</term><term>Phytophthora (genetics)</term><term>Phytophthora (physiology)</term><term>Plant Diseases (parasitology)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Fruit (parasitologie)</term><term>Génomique (MeSH)</term><term>Litchi (parasitologie)</term><term>Maladies des plantes (parasitologie)</term><term>Phylogenèse (MeSH)</term><term>Phytophthora (classification)</term><term>Phytophthora (génétique)</term><term>Phytophthora (physiologie)</term><term>Structure tertiaire des protéines (MeSH)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Fruit</term><term>Litchi</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Fruit</term><term>Litchi</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genomics</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Génomique</term><term>Phylogenèse</term><term>Phytophthora</term><term>Structure tertiaire des protéines</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27183038</PMID><DateCompleted><Year>2016</Year><Month>09</Month><Day>08</Day></DateCompleted><DateRevised><Year>2016</Year><Month>07</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>29</Volume><Issue>7</Issue><PubDate><Year>2016</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics.</ArticleTitle><Pagination><MedlinePgn>573-83</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/MPMI-03-16-0056-R</ELocationID><Abstract><AbstractText>On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Wenwu</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Danyu</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Delong</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pu</LastName><ForeName>Tianhuizi</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Zide</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>3 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhengguang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Xiaobo</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.; and.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yuanchao</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>06</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Plant Microbe Interact</MedlineTA><NlmUniqueID>9107902</NlmUniqueID><ISSNLinking>0894-0282</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005638" MajorTopicYN="N">Fruit</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="N">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032125" MajorTopicYN="N">Litchi</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>5</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>5</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27183038</ArticleId><ArticleId IdType="doi">10.1094/MPMI-03-16-0056-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li><li>États-Unis</li></country><region><li>Guangdong</li><li>Oregon</li></region><settlement><li>Jiangmen</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name></noRegion><name sortKey="Jiang, Zide" sort="Jiang, Zide" uniqKey="Jiang Z" first="Zide" last="Jiang">Zide Jiang</name><name sortKey="Li, Delong" sort="Li, Delong" uniqKey="Li D" first="Delong" last="Li">Delong Li</name><name sortKey="Pu, Tianhuizi" sort="Pu, Tianhuizi" uniqKey="Pu T" first="Tianhuizi" last="Pu">Tianhuizi Pu</name><name sortKey="Shen, Danyu" sort="Shen, Danyu" uniqKey="Shen D" first="Danyu" last="Shen">Danyu Shen</name><name sortKey="Wang, Yang" sort="Wang, Yang" uniqKey="Wang Y" first="Yang" last="Wang">Yang Wang</name><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><name sortKey="Zhang, Zhengguang" sort="Zhang, Zhengguang" uniqKey="Zhang Z" first="Zhengguang" last="Zhang">Zhengguang Zhang</name><name sortKey="Zheng, Xiaobo" sort="Zheng, Xiaobo" uniqKey="Zheng X" first="Xiaobo" last="Zheng">Xiaobo Zheng</name></country><country name="États-Unis"><region name="Oregon"><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. 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