An integrated BAC and genome sequence physical map of Phytophthora sojae.
Identifieur interne : 000299 ( Main/Exploration ); précédent : 000298; suivant : 000300An integrated BAC and genome sequence physical map of Phytophthora sojae.
Auteurs : Xuemin Zhang [États-Unis] ; Chantel Scheuring ; Sucheta Tripathy ; Zhanyou Xu ; Chengcang Wu ; Angela Ko ; S Ken Tian ; Felipe Arredondo ; Mi-Kyung Lee ; Felipe A. Santos ; Rays H Y. Jiang ; Hong-Bin Zhang ; Brett M. TylerSource :
- Molecular plant-microbe interactions : MPMI [ 0894-0282 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora.
- normes : Cartographie de contigs.
- Banque génomique, Chromosomes artificiels de bactérie, Famille multigénique, Génome, Profilage d'ADN.
English descriptors
- KwdEn :
- MESH :
- genetics : Phytophthora.
- standards : Contig Mapping.
- Chromosomes, Artificial, Bacterial, DNA Fingerprinting, Genome, Genomic Library, Multigene Family.
Abstract
Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.
DOI: 10.1094/MPMI-19-1302
PubMed: 17153914
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Santos</name></author><author><name sortKey="Jiang, Rays H Y" sort="Jiang, Rays H Y" uniqKey="Jiang R" first="Rays H Y" last="Jiang">Rays H Y. Jiang</name></author><author><name sortKey="Zhang, Hong Bin" sort="Zhang, Hong Bin" uniqKey="Zhang H" first="Hong-Bin" last="Zhang">Hong-Bin Zhang</name></author><author><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name></author></analytic><series><title level="j">Molecular plant-microbe interactions : MPMI</title><idno type="ISSN">0894-0282</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Artificial, Bacterial (MeSH)</term><term>Contig Mapping (standards)</term><term>DNA Fingerprinting (MeSH)</term><term>Genome (MeSH)</term><term>Genomic Library (MeSH)</term><term>Multigene Family (MeSH)</term><term>Phytophthora (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Banque génomique (MeSH)</term><term>Cartographie de contigs (normes)</term><term>Chromosomes artificiels de bactérie (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Génome (MeSH)</term><term>Phytophthora (génétique)</term><term>Profilage d'ADN (MeSH)</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="normes" xml:lang="fr"><term>Cartographie de contigs</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Contig Mapping</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Artificial, Bacterial</term><term>DNA Fingerprinting</term><term>Genome</term><term>Genomic Library</term><term>Multigene Family</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Banque génomique</term><term>Chromosomes artificiels de bactérie</term><term>Famille multigénique</term><term>Génome</term><term>Profilage d'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17153914</PMID><DateCompleted><Year>2007</Year><Month>02</Month><Day>12</Day></DateCompleted><DateRevised><Year>2006</Year><Month>12</Month><Day>12</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0894-0282</ISSN><JournalIssue CitedMedium="Print"><Volume>19</Volume><Issue>12</Issue><PubDate><Year>2006</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular plant-microbe interactions : MPMI</Title><ISOAbbreviation>Mol Plant Microbe Interact</ISOAbbreviation></Journal><ArticleTitle>An integrated BAC and genome sequence physical map of Phytophthora sojae.</ArticleTitle><Pagination><MedlinePgn>1302-10</MedlinePgn></Pagination><Abstract><AbstractText>Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xuemin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0477, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scheuring</LastName><ForeName>Chantel</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Tripathy</LastName><ForeName>Sucheta</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Zhanyou</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Chengcang</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Ko</LastName><ForeName>Angela</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>S Ken</ForeName><Initials>SK</Initials></Author><Author ValidYN="Y"><LastName>Arredondo</LastName><ForeName>Felipe</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Mi-Kyung</ForeName><Initials>MK</Initials></Author><Author ValidYN="Y"><LastName>Santos</LastName><ForeName>Felipe A</ForeName><Initials>FA</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Rays H Y</ForeName><Initials>RH</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Hong-Bin</ForeName><Initials>HB</Initials></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></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="D022202" MajorTopicYN="Y">Chromosomes, Artificial, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020451" MajorTopicYN="Y">Contig Mapping</DescriptorName><QualifierName UI="Q000592" MajorTopicYN="N">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016172" MajorTopicYN="N">DNA Fingerprinting</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="Y">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015698" MajorTopicYN="N">Genomic Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>12</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>2</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>12</Month><Day>13</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">17153914</ArticleId><ArticleId IdType="doi">10.1094/MPMI-19-1302</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Virginie</li></region></list><tree><noCountry><name sortKey="Arredondo, Felipe" sort="Arredondo, Felipe" uniqKey="Arredondo F" first="Felipe" last="Arredondo">Felipe Arredondo</name><name sortKey="Jiang, Rays H Y" sort="Jiang, Rays H Y" uniqKey="Jiang R" first="Rays H Y" last="Jiang">Rays H Y. Jiang</name><name sortKey="Ko, Angela" sort="Ko, Angela" uniqKey="Ko A" first="Angela" last="Ko">Angela Ko</name><name sortKey="Lee, Mi Kyung" sort="Lee, Mi Kyung" uniqKey="Lee M" first="Mi-Kyung" last="Lee">Mi-Kyung Lee</name><name sortKey="Santos, Felipe A" sort="Santos, Felipe A" uniqKey="Santos F" first="Felipe A" last="Santos">Felipe A. Santos</name><name sortKey="Scheuring, Chantel" sort="Scheuring, Chantel" uniqKey="Scheuring C" first="Chantel" last="Scheuring">Chantel Scheuring</name><name sortKey="Tian, S Ken" sort="Tian, S Ken" uniqKey="Tian S" first="S Ken" last="Tian">S Ken Tian</name><name sortKey="Tripathy, Sucheta" sort="Tripathy, Sucheta" uniqKey="Tripathy S" first="Sucheta" last="Tripathy">Sucheta Tripathy</name><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name><name sortKey="Wu, Chengcang" sort="Wu, Chengcang" uniqKey="Wu C" first="Chengcang" last="Wu">Chengcang Wu</name><name sortKey="Xu, Zhanyou" sort="Xu, Zhanyou" uniqKey="Xu Z" first="Zhanyou" last="Xu">Zhanyou Xu</name><name sortKey="Zhang, Hong Bin" sort="Zhang, Hong Bin" uniqKey="Zhang H" first="Hong-Bin" last="Zhang">Hong-Bin Zhang</name></noCountry><country name="États-Unis"><region name="Virginie"><name sortKey="Zhang, Xuemin" sort="Zhang, Xuemin" uniqKey="Zhang X" first="Xuemin" last="Zhang">Xuemin Zhang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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