An overview of the apple genome through BAC end sequence analysis.
Identifieur interne : 003994 ( Main/Exploration ); précédent : 003993; suivant : 003995An overview of the apple genome through BAC end sequence analysis.
Auteurs : Yuepeng Han [États-Unis] ; Schuyler S. KorbanSource :
- Plant molecular biology [ 0167-4412 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- chemical : DNA Transposable Elements, Retroelements.
- genetics : Malus.
- Chromosomes, Artificial, Bacterial, Genome, Plant, Microsatellite Repeats, Physical Chromosome Mapping, Sequence Analysis, DNA.
Abstract
The apple, Malus x domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of approximately 2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in approximately 21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.
DOI: 10.1007/s11103-008-9321-9
PubMed: 18521706
Affiliations:
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Le document en format XML
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Korban</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18521706</idno><idno type="pmid">18521706</idno><idno type="doi">10.1007/s11103-008-9321-9</idno><idno type="wicri:Area/Main/Corpus">003870</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003870</idno><idno type="wicri:Area/Main/Curation">003870</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003870</idno><idno type="wicri:Area/Main/Exploration">003870</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">An overview of the apple genome through BAC end sequence analysis.</title><author><name sortKey="Han, Yuepeng" sort="Han, Yuepeng" uniqKey="Han Y" first="Yuepeng" last="Han">Yuepeng Han</name><affiliation wicri:level="2"><nlm:affiliation>Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Korban, Schuyler S" sort="Korban, Schuyler S" uniqKey="Korban S" first="Schuyler S" last="Korban">Schuyler S. Korban</name></author></analytic><series><title level="j">Plant molecular biology</title><idno type="ISSN">0167-4412</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Artificial, Bacterial (MeSH)</term><term>DNA Transposable Elements (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Malus (genetics)</term><term>Microsatellite Repeats (MeSH)</term><term>Physical Chromosome Mapping (MeSH)</term><term>Plant Proteins (genetics)</term><term>Retroelements (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Cartographie physique de chromosome (MeSH)</term><term>Chromosomes artificiels de bactérie (MeSH)</term><term>Génome végétal (MeSH)</term><term>Malus (génétique)</term><term>Protéines végétales (génétique)</term><term>Répétitions microsatellites (MeSH)</term><term>Rétroéléments (MeSH)</term><term>Éléments transposables d'ADN (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Transposable Elements</term><term>Retroelements</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Malus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Malus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Artificial, Bacterial</term><term>Genome, Plant</term><term>Microsatellite Repeats</term><term>Physical Chromosome Mapping</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie physique de chromosome</term><term>Chromosomes artificiels de bactérie</term><term>Génome végétal</term><term>Répétitions microsatellites</term><term>Rétroéléments</term><term>Éléments transposables d'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The apple, Malus x domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of approximately 2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in approximately 21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18521706</PMID><DateCompleted><Year>2008</Year><Month>08</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0167-4412</ISSN><JournalIssue CitedMedium="Print"><Volume>67</Volume><Issue>6</Issue><PubDate><Year>2008</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Plant molecular biology</Title><ISOAbbreviation>Plant Mol Biol</ISOAbbreviation></Journal><ArticleTitle>An overview of the apple genome through BAC end sequence analysis.</ArticleTitle><Pagination><MedlinePgn>581-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11103-008-9321-9</ELocationID><Abstract><AbstractText>The apple, Malus x domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of approximately 2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in approximately 21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Han</LastName><ForeName>Yuepeng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Korban</LastName><ForeName>Schuyler S</ForeName><Initials>SS</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>06</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Plant Mol 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Korban</name></noCountry><country name="États-Unis"><region name="Illinois"><name sortKey="Han, Yuepeng" sort="Han, Yuepeng" uniqKey="Han Y" first="Yuepeng" last="Han">Yuepeng Han</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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