Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
Identifieur interne : 003604 ( Main/Exploration ); précédent : 003603; suivant : 003605Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
Auteurs : Juliane C. Dohm [Allemagne] ; Cornelia Lange ; Richard Reinhardt ; Heinz HimmelbauerSource :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2009.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Alignement de séquences (MeSH), Analyse de séquence d'ADN (MeSH), Banque de gènes (MeSH), Beta vulgaris (génétique), Chromosomes artificiels de bactérie (MeSH), Chromosomes de plante (MeSH), Composition en bases nucléiques (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Génotype (MeSH), Haplotypes (MeSH), Ordre des gènes (MeSH), Polymorphisme génétique (MeSH), Synténie (MeSH).
- MESH :
- génétique : ADN des plantes, Beta vulgaris.
- Alignement de séquences, Analyse de séquence d'ADN, Banque de gènes, Chromosomes artificiels de bactérie, Chromosomes de plante, Composition en bases nucléiques, Gènes de plante, Génome végétal, Génotype, Haplotypes, Ordre des gènes, Polymorphisme génétique, Synténie.
English descriptors
- KwdEn :
- Base Composition (MeSH), Beta vulgaris (genetics), Chromosomes, Artificial, Bacterial (MeSH), Chromosomes, Plant (MeSH), DNA, Plant (genetics), Gene Library (MeSH), Gene Order (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Genotype (MeSH), Haplotypes (MeSH), Polymorphism, Genetic (MeSH), Sequence Alignment (MeSH), Sequence Analysis, DNA (MeSH), Synteny (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- genetics : Beta vulgaris.
- Base Composition, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Gene Library, Gene Order, Genes, Plant, Genome, Plant, Genotype, Haplotypes, Polymorphism, Genetic, Sequence Alignment, Sequence Analysis, DNA, Synteny.
Abstract
We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined, of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.
DOI: 10.1111/j.1365-313X.2008.03665.x
PubMed: 18764921
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.</title><author><name sortKey="Dohm, Juliane C" sort="Dohm, Juliane C" uniqKey="Dohm J" first="Juliane C" last="Dohm">Juliane C. Dohm</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Lange, Cornelia" sort="Lange, Cornelia" uniqKey="Lange C" first="Cornelia" last="Lange">Cornelia Lange</name></author><author><name sortKey="Reinhardt, Richard" sort="Reinhardt, Richard" uniqKey="Reinhardt R" first="Richard" last="Reinhardt">Richard Reinhardt</name></author><author><name sortKey="Himmelbauer, Heinz" sort="Himmelbauer, Heinz" uniqKey="Himmelbauer H" first="Heinz" last="Himmelbauer">Heinz Himmelbauer</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:18764921</idno><idno type="pmid">18764921</idno><idno type="doi">10.1111/j.1365-313X.2008.03665.x</idno><idno type="wicri:Area/Main/Corpus">003804</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003804</idno><idno type="wicri:Area/Main/Curation">003804</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003804</idno><idno type="wicri:Area/Main/Exploration">003804</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.</title><author><name sortKey="Dohm, Juliane C" sort="Dohm, Juliane C" uniqKey="Dohm J" first="Juliane C" last="Dohm">Juliane C. Dohm</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Lange, Cornelia" sort="Lange, Cornelia" uniqKey="Lange C" first="Cornelia" last="Lange">Cornelia Lange</name></author><author><name sortKey="Reinhardt, Richard" sort="Reinhardt, Richard" uniqKey="Reinhardt R" first="Richard" last="Reinhardt">Richard Reinhardt</name></author><author><name sortKey="Himmelbauer, Heinz" sort="Himmelbauer, Heinz" uniqKey="Himmelbauer H" first="Heinz" last="Himmelbauer">Heinz Himmelbauer</name></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition (MeSH)</term><term>Beta vulgaris (genetics)</term><term>Chromosomes, Artificial, Bacterial (MeSH)</term><term>Chromosomes, Plant (MeSH)</term><term>DNA, Plant (genetics)</term><term>Gene Library (MeSH)</term><term>Gene Order (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Haplotypes (MeSH)</term><term>Polymorphism, Genetic (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Synteny (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Alignement de séquences (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Banque de gènes (MeSH)</term><term>Beta vulgaris (génétique)</term><term>Chromosomes artificiels de bactérie (MeSH)</term><term>Chromosomes de plante (MeSH)</term><term>Composition en bases nucléiques (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Génotype (MeSH)</term><term>Haplotypes (MeSH)</term><term>Ordre des gènes (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Synténie (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Beta vulgaris</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Beta vulgaris</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Composition</term><term>Chromosomes, Artificial, Bacterial</term><term>Chromosomes, Plant</term><term>Gene Library</term><term>Gene Order</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Genotype</term><term>Haplotypes</term><term>Polymorphism, Genetic</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Banque de gènes</term><term>Chromosomes artificiels de bactérie</term><term>Chromosomes de plante</term><term>Composition en bases nucléiques</term><term>Gènes de plante</term><term>Génome végétal</term><term>Génotype</term><term>Haplotypes</term><term>Ordre des gènes</term><term>Polymorphisme génétique</term><term>Synténie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined, of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18764921</PMID><DateCompleted><Year>2009</Year><Month>02</Month><Day>05</Day></DateCompleted><DateRevised><Year>2009</Year><Month>01</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>57</Volume><Issue>1</Issue><PubDate><Year>2009</Year><Month>Jan</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.</ArticleTitle><Pagination><MedlinePgn>14-26</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1365-313X.2008.03665.x</ELocationID><Abstract><AbstractText>We characterized two overlapping sugar beet (Beta vulgaris) bacterial artificial chromosome (BAC) clones representing different haplotypes. A total of 254 kbp of the genomic sequence was determined, of which the two BACs share 92 kbp. Eleven of 15 genes discovered in the sequenced interval locate to the overlap region. The haplotypes differ in exons by 1% (nucleotide level) and in non-coding regions by 9% (6% mismatches, 3% gaps; alignable regions only). Large indels or high sequence divergence comprised 11% of either sequence. Of such indels, 68 and 45%, respectively, could be attributed to haplotype-specific integration of transposable elements. We identified novel repeat candidates by comparing the two BAC sequences to a set of genomic sugar beet sequences. Synteny was found with Arabidopsis chromosome 1 (At1), At2 and At4, Medicago chromosome 7, Vitis chromosome 15 and paralogous regions on poplar chromosomes II and XIV.</AbstractText></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, Ihnestrasse 63-73, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lange</LastName><ForeName>Cornelia</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Reinhardt</LastName><ForeName>Richard</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Himmelbauer</LastName><ForeName>Heinz</ForeName><Initials>H</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>08</Month><Day>29</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></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001482" MajorTopicYN="N">Base Composition</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D027461" MajorTopicYN="N">Beta vulgaris</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023061" MajorTopicYN="N">Gene Order</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="Y">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011110" MajorTopicYN="N">Polymorphism, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="Y">Synteny</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>9</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>2</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>9</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18764921</ArticleId><ArticleId IdType="pii">TPJ3665</ArticleId><ArticleId IdType="doi">10.1111/j.1365-313X.2008.03665.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="Himmelbauer, Heinz" sort="Himmelbauer, Heinz" uniqKey="Himmelbauer H" first="Heinz" last="Himmelbauer">Heinz Himmelbauer</name><name sortKey="Lange, Cornelia" sort="Lange, Cornelia" uniqKey="Lange C" first="Cornelia" last="Lange">Cornelia Lange</name><name sortKey="Reinhardt, Richard" sort="Reinhardt, Richard" uniqKey="Reinhardt R" first="Richard" last="Reinhardt">Richard Reinhardt</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. Dohm</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PoplarV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003604 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003604 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:18764921
|texte= Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:18764921" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |