Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).
Identifieur interne : 002971 ( Main/Exploration ); précédent : 002970; suivant : 002972Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).
Auteurs : Juliane C. Dohm [Allemagne] ; Cornelia Lange ; Daniela Holtgr We ; Thomas Rosleff Sörensen ; Dietrich Borchardt ; Britta Schulz ; Hans Lehrach ; Bernd Weisshaar ; Heinz HimmelbauerSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2012.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Beta vulgaris (génétique), Cartographie chromosomique (MeSH), Cartographie physique de chromosome (MeSH), Chromosomes artificiels de bactérie (MeSH), Gènes de plante (génétique), Génome végétal (génétique), Génomique (MeSH), Liaison génétique (MeSH), Magnoliopsida (génétique), Marqueurs génétiques (génétique), Polymorphisme de nucléotide simple (génétique), Polyploïdie (MeSH), Synténie (génétique), Séquence nucléotidique (MeSH), Étiquettes de séquences exprimées (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : ADN des plantes, Beta vulgaris, Gènes de plante, Génome végétal, Magnoliopsida, Marqueurs génétiques, Polymorphisme de nucléotide simple, Synténie.
- Analyse de séquence d'ADN, Cartographie chromosomique, Cartographie physique de chromosome, Chromosomes artificiels de bactérie, Génomique, Liaison génétique, Polyploïdie, Séquence nucléotidique, Étiquettes de séquences exprimées, Évolution moléculaire.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Beta vulgaris (genetics), Chromosome Mapping (MeSH), Chromosomes, Artificial, Bacterial (MeSH), DNA, Plant (genetics), Evolution, Molecular (MeSH), Expressed Sequence Tags (MeSH), Genes, Plant (genetics), Genetic Linkage (MeSH), Genetic Markers (genetics), Genome, Plant (genetics), Genomics (MeSH), Magnoliopsida (genetics), Physical Chromosome Mapping (MeSH), Polymorphism, Single Nucleotide (genetics), Polyploidy (MeSH), Sequence Analysis, DNA (MeSH), Synteny (genetics).
- MESH :
- chemical , genetics : DNA, Plant, Genetic Markers.
- genetics : Beta vulgaris, Genes, Plant, Genome, Plant, Magnoliopsida, Polymorphism, Single Nucleotide, Synteny.
- Base Sequence, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Evolution, Molecular, Expressed Sequence Tags, Genetic Linkage, Genomics, Physical Chromosome Mapping, Polyploidy, Sequence Analysis, DNA.
Abstract
Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.
DOI: 10.1111/j.1365-313X.2011.04898.x
PubMed: 22211633
Affiliations:
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moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22211633</PMID><DateCompleted><Year>2012</Year><Month>11</Month><Day>26</Day></DateCompleted><DateRevised><Year>2017</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>70</Volume><Issue>3</Issue><PubDate><Year>2012</Year><Month>May</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).</ArticleTitle><Pagination><MedlinePgn>528-40</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1365-313X.2011.04898.x</ELocationID><Abstract><AbstractText>Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.</AbstractText><CopyrightInformation>© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dohm</LastName><ForeName>Juliane C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lange</LastName><ForeName>Cornelia</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Holtgräwe</LastName><ForeName>Daniela</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Sörensen</LastName><ForeName>Thomas Rosleff</ForeName><Initials>TR</Initials></Author><Author ValidYN="Y"><LastName>Borchardt</LastName><ForeName>Dietrich</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Schulz</LastName><ForeName>Britta</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Lehrach</LastName><ForeName>Hans</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Weisshaar</LastName><ForeName>Bernd</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Himmelbauer</LastName><ForeName>Heinz</ForeName><Initials>H</Initials></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>2012</Year><Month>02</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Plant J. 2012 Jul;71(1):182</RefSource></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D027461" MajorTopicYN="N">Beta vulgaris</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="Y">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008040" MajorTopicYN="N">Genetic Linkage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020161" MajorTopicYN="N">Physical Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011123" MajorTopicYN="N">Polyploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="N">Synteny</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>1</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>1</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>12</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22211633</ArticleId><ArticleId IdType="doi">10.1111/j.1365-313X.2011.04898.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country><region><li>Berlin</li></region><settlement><li>Berlin</li></settlement></list><tree><noCountry><name sortKey="Borchardt, Dietrich" sort="Borchardt, Dietrich" uniqKey="Borchardt D" first="Dietrich" last="Borchardt">Dietrich Borchardt</name><name sortKey="Himmelbauer, Heinz" sort="Himmelbauer, Heinz" uniqKey="Himmelbauer H" first="Heinz" last="Himmelbauer">Heinz Himmelbauer</name><name sortKey="Holtgr We, Daniela" sort="Holtgr We, Daniela" uniqKey="Holtgr We D" first="Daniela" last="Holtgr We">Daniela Holtgr We</name><name sortKey="Lange, Cornelia" sort="Lange, Cornelia" uniqKey="Lange C" first="Cornelia" last="Lange">Cornelia Lange</name><name sortKey="Lehrach, Hans" sort="Lehrach, Hans" uniqKey="Lehrach H" first="Hans" last="Lehrach">Hans Lehrach</name><name sortKey="Schulz, Britta" sort="Schulz, Britta" uniqKey="Schulz B" first="Britta" last="Schulz">Britta Schulz</name><name sortKey="Sorensen, Thomas Rosleff" sort="Sorensen, Thomas Rosleff" uniqKey="Sorensen T" first="Thomas Rosleff" last="Sörensen">Thomas Rosleff Sörensen</name><name sortKey="Weisshaar, Bernd" sort="Weisshaar, Bernd" uniqKey="Weisshaar B" first="Bernd" last="Weisshaar">Bernd Weisshaar</name></noCountry><country name="Allemagne"><region name="Berlin"><name sortKey="Dohm, Juliane C" sort="Dohm, Juliane C" uniqKey="Dohm J" first="Juliane C" last="Dohm">Juliane C. 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