A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database
Identifieur interne : 000355 ( Main/Exploration ); précédent : 000354; suivant : 000356A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database
Auteurs : Ezio Portis [Italie] ; Flavio Portis [Italie] ; Luisa Valente [Italie] ; Andrea Moglia [Italie] ; Lorenzo Barchi [Italie] ; Sergio Lanteri [Italie] ; Alberto Acquadro [Italie]Source :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
The recently acquired genome sequence of globe artichoke (
Url:
DOI: 10.1371/journal.pone.0162841
PubMed: 27648830
PubMed Central: 5029897
Affiliations:
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Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27648830</idno><idno type="pmc">5029897</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029897</idno><idno type="RBID">PMC:5029897</idno><idno type="doi">10.1371/journal.pone.0162841</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">001099</idno><idno type="wicri:Area/Pmc/Curation">001098</idno><idno type="wicri:Area/Pmc/Checkpoint">000281</idno><idno type="wicri:Area/Ncbi/Merge">002177</idno><idno type="wicri:Area/Ncbi/Curation">002177</idno><idno type="wicri:Area/Ncbi/Checkpoint">002177</idno><idno type="wicri:Area/Main/Merge">000355</idno><idno type="wicri:Area/Main/Curation">000355</idno><idno type="wicri:Area/Main/Exploration">000355</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database</title><author><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Portis, Flavio" sort="Portis, Flavio" uniqKey="Portis F" first="Flavio" last="Portis">Flavio Portis</name><affiliation wicri:level="3"><nlm:aff id="aff002"><addr-line>Yebokey – User Experience Design and Web Development, I-10134, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Yebokey – User Experience Design and Web Development, I-10134, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Valente, Luisa" sort="Valente, Luisa" uniqKey="Valente L" first="Luisa" last="Valente">Luisa Valente</name><affiliation wicri:level="3"><nlm:aff id="aff002"><addr-line>Yebokey – User Experience Design and Web Development, I-10134, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Yebokey – User Experience Design and Web Development, I-10134, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Moglia, Andrea" sort="Moglia, Andrea" uniqKey="Moglia A" first="Andrea" last="Moglia">Andrea Moglia</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Barchi, Lorenzo" sort="Barchi, Lorenzo" uniqKey="Barchi L" first="Lorenzo" last="Barchi">Lorenzo Barchi</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author><author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><affiliation wicri:level="3"><nlm:aff id="aff001"><addr-line>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino</wicri:regionArea><placeName><settlement type="city">Turin</settlement><region type="région" nuts="2">Piémont</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The recently acquired genome sequence of globe artichoke (<italic>Cynara cardunculus</italic> var. <italic>scolymus</italic>) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (<italic>Helianthus annuus</italic>) and horseweed (<italic>Conyza canadensis</italic>)) included in the study. Finally, a database, called “<italic>Cynara cardunculus</italic> MicroSatellite DataBase” (<italic>CyMSatDB</italic>) was developed to provide a searchable interface to the SSR data. <italic>CyMSatDB</italic> facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic <italic>vs</italic> genic context, perfect <italic>vs</italic> imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an <italic>in silico</italic> based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Portis, E" uniqKey="Portis E">E Portis</name></author><author><name sortKey="Mauromicale, G" uniqKey="Mauromicale G">G Mauromicale</name></author><author><name sortKey="Barchi, L" uniqKey="Barchi L">L Barchi</name></author><author><name sortKey="Mauro, R" uniqKey="Mauro R">R Mauro</name></author><author><name sortKey="Lanteri, S" uniqKey="Lanteri S">S Lanteri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mauro, R" uniqKey="Mauro R">R Mauro</name></author><author><name sortKey="Portis, E" uniqKey="Portis E">E Portis</name></author><author><name sortKey="Acquadro, A" uniqKey="Acquadro A">A Acquadro</name></author><author><name sortKey="Lombardo, S" 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Estrella L">L Herrera-Estrella</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cardle, L" uniqKey="Cardle L">L Cardle</name></author><author><name sortKey="Ramsay, L" uniqKey="Ramsay L">L Ramsay</name></author><author><name sortKey="Milbourne, D" uniqKey="Milbourne D">D Milbourne</name></author><author><name sortKey="Macaulay, M" uniqKey="Macaulay M">M Macaulay</name></author><author><name sortKey="Marshall, D" uniqKey="Marshall D">D Marshall</name></author><author><name sortKey="Waugh, R" uniqKey="Waugh R">R Waugh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mondal, T" uniqKey="Mondal T">T Mondal</name></author><author><name sortKey="Ganie, S" uniqKey="Ganie S">S Ganie</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li></country><region><li>Piémont</li></region><settlement><li>Turin</li></settlement></list><tree><country name="Italie"><region name="Piémont"><name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name></region><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name><name sortKey="Barchi, Lorenzo" sort="Barchi, Lorenzo" uniqKey="Barchi L" first="Lorenzo" last="Barchi">Lorenzo Barchi</name><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name><name sortKey="Moglia, Andrea" sort="Moglia, Andrea" uniqKey="Moglia A" first="Andrea" last="Moglia">Andrea Moglia</name><name sortKey="Portis, Flavio" sort="Portis, Flavio" uniqKey="Portis F" first="Flavio" last="Portis">Flavio Portis</name><name sortKey="Valente, Luisa" sort="Valente, Luisa" uniqKey="Valente L" first="Luisa" last="Valente">Luisa Valente</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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