Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.
Identifieur interne : 002F95 ( Main/Exploration ); précédent : 002F94; suivant : 002F96Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.
Auteurs : Patricia Faivre Rampant [France] ; Isabelle Lesur ; Clément Boussardon ; Frédérique Bitton ; Marie-Laure Martin-Magniette ; Catherine Bodénès ; Grégoire Le Provost ; Hélène Bergès ; Sylvia Fluch ; Antoine Kremer ; Christophe PlomionSource :
- BMC genomics [ 1471-2164 ] ; 2011.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Annotation de séquence moléculaire (MeSH), Banque génomique (MeSH), Cartographie chromosomique (MeSH), Chromosomes artificiels de bactérie (génétique), Cytoplasme (génétique), Génome végétal (génétique), Génomique (MeSH), Quercus (cytologie), Quercus (génétique), Répétitions minisatellites (génétique).
- MESH :
English descriptors
- KwdEn :
- Chromosome Mapping (MeSH), Chromosomes, Artificial, Bacterial (genetics), Cytoplasm (genetics), DNA, Plant (genetics), Genome, Plant (genetics), Genomic Library (MeSH), Genomics (MeSH), Minisatellite Repeats (genetics), Molecular Sequence Annotation (MeSH), Quercus (cytology), Quercus (genetics), Sequence Analysis, DNA (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- cytology : Quercus.
- genetics : Chromosomes, Artificial, Bacterial, Cytoplasm, Genome, Plant, Minisatellite Repeats, Quercus.
- Chromosome Mapping, Genomic Library, Genomics, Molecular Sequence Annotation, Sequence Analysis, DNA.
Abstract
BACKGROUND
One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences.
RESULTS
The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera.
CONCLUSIONS
This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.
DOI: 10.1186/1471-2164-12-292
PubMed: 21645357
PubMed Central: PMC3132169
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Artificial, Bacterial</term><term>Cytoplasm</term><term>Genome, Plant</term><term>Minisatellite Repeats</term><term>Quercus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Chromosomes artificiels de bactérie</term><term>Cytoplasme</term><term>Génome végétal</term><term>Quercus</term><term>Répétitions minisatellites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genomic Library</term><term>Genomics</term><term>Molecular Sequence Annotation</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Annotation de séquence moléculaire</term><term>Banque génomique</term><term>Cartographie chromosomique</term><term>Génomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21645357</PMID><DateCompleted><Year>2011</Year><Month>09</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><PubDate><Year>2011</Year><Month>Jun</Month><Day>06</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome.</ArticleTitle><Pagination><MedlinePgn>292</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-12-292</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Faivre Rampant</LastName><ForeName>Patricia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>INRA, URGV, Plant Genomics Research, F-91057 Evry, France. faivre@evry.inra.fr</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lesur</LastName><ForeName>Isabelle</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Boussardon</LastName><ForeName>Clément</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Bitton</LastName><ForeName>Frédérique</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Martin-Magniette</LastName><ForeName>Marie-Laure</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Bodénès</LastName><ForeName>Catherine</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Le Provost</LastName><ForeName>Grégoire</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Bergès</LastName><ForeName>Hélène</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Fluch</LastName><ForeName>Sylvia</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Kremer</LastName><ForeName>Antoine</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Plomion</LastName><ForeName>Christophe</ForeName><Initials>C</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>2011</Year><Month>06</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D022202" MajorTopicYN="N">Chromosomes, Artificial, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003593" MajorTopicYN="N">Cytoplasm</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</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="D015698" MajorTopicYN="N">Genomic Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018598" MajorTopicYN="N">Minisatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029963" MajorTopicYN="N">Quercus</DescriptorName><QualifierName UI="Q000166" MajorTopicYN="N">cytology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="Y">Sequence Analysis, 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sort="Martin Magniette, Marie Laure" uniqKey="Martin Magniette M" first="Marie-Laure" last="Martin-Magniette">Marie-Laure Martin-Magniette</name><name sortKey="Plomion, Christophe" sort="Plomion, Christophe" uniqKey="Plomion C" first="Christophe" last="Plomion">Christophe Plomion</name></noCountry><country name="France"><region name="Île-de-France"><name sortKey="Faivre Rampant, Patricia" sort="Faivre Rampant, Patricia" uniqKey="Faivre Rampant P" first="Patricia" last="Faivre Rampant">Patricia Faivre Rampant</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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