RAD tag sequencing as a source of SNP markers in Cynara cardunculus L
Identifieur interne : 001288 ( Pmc/Checkpoint ); précédent : 001287; suivant : 001289RAD tag sequencing as a source of SNP markers in Cynara cardunculus L
Auteurs : Davide Scaglione [Italie] ; Alberto Acquadro [Italie] ; Ezio Portis [Italie] ; Matteo Tirone [Italie] ; Steven J. Knapp ; Sergio Lanteri [Italie]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Abstract
The globe artichoke (
RAD tags were sequenced from the genomic DNA of three
The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.
Url:
DOI: 10.1186/1471-2164-13-3
PubMed: 22214349
PubMed Central: 3269995
Affiliations:
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PMC:3269995Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">RAD tag sequencing as a source of SNP markers in <italic>Cynara cardunculus </italic>
L</title>
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<author><name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name>
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<author><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name>
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<author><name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name>
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<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2012">2012</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The globe artichoke (<italic>Cynara cardunculus </italic>
L. var. <italic>scolymus</italic>
) genome is relatively poorly explored, especially compared to those of the other major <italic>Asteraceae </italic>
crops sunflower and lettuce. No SNP markers are in the public domain. We have combined the recently developed restriction-site associated DNA (RAD) approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for <italic>C. cardunculus</italic>
.</p>
</sec>
<sec><title>Results</title>
<p>RAD tags were sequenced from the genomic DNA of three <italic>C. cardunculus </italic>
mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. An assembly based on paired ends produced ~6.0 Mbp of genomic sequence, separated into ~19,000 contigs (mean length 312 bp), of which ~21% were fragments of putative coding sequence. The shared sequences allowed for the discovery of ~34,000 SNPs and nearly 800 indels, equivalent to a SNP frequency of 5.6 per 1,000 nt, and an indel frequency of 0.2 per 1,000 nt. A sample of heterozygous SNP loci was mapped by CAPS assays and this exercise provided validation of our mining criteria. The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of <italic>C. cardunculus</italic>
, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the <italic>C. cardunculus </italic>
genome generated by RAD sampling.</p>
</sec>
<sec><title>Conclusion</title>
<p>The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id>
<journal-title-group><journal-title>BMC Genomics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2164</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22214349</article-id>
<article-id pub-id-type="pmc">3269995</article-id>
<article-id pub-id-type="publisher-id">1471-2164-13-3</article-id>
<article-id pub-id-type="doi">10.1186/1471-2164-13-3</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>RAD tag sequencing as a source of SNP markers in <italic>Cynara cardunculus </italic>
L</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Scaglione</surname>
<given-names>Davide</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>davide.scaglione@unito.it</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Acquadro</surname>
<given-names>Alberto</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>alberto.acquadro@unito.it</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Portis</surname>
<given-names>Ezio</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>ezio.portis@unito.it</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Tirone</surname>
<given-names>Matteo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>matteo.tirone@unito.it</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Knapp</surname>
<given-names>Steven J</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>sjknapp@uga.edu</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A6"><name><surname>Lanteri</surname>
<given-names>Sergio</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>sergio.lanteri@unito.it</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci 44, 10095 Grugliasco (Torino), Italy</aff>
<aff id="I2"><label>2</label>
Institute for Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd., 30602 Athens, Georgia USA</aff>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>3</day>
<month>1</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<fpage>3</fpage>
<lpage>3</lpage>
<history><date date-type="received"><day>6</day>
<month>8</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>3</day>
<month>1</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2012 Scaglione et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Scaglione et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2164/13/3"></self-uri>
<abstract><sec><title>Background</title>
<p>The globe artichoke (<italic>Cynara cardunculus </italic>
L. var. <italic>scolymus</italic>
) genome is relatively poorly explored, especially compared to those of the other major <italic>Asteraceae </italic>
crops sunflower and lettuce. No SNP markers are in the public domain. We have combined the recently developed restriction-site associated DNA (RAD) approach with the Illumina DNA sequencing platform to effect the rapid and mass discovery of SNP markers for <italic>C. cardunculus</italic>
.</p>
</sec>
<sec><title>Results</title>
<p>RAD tags were sequenced from the genomic DNA of three <italic>C. cardunculus </italic>
mapping population parents, generating 9.7 million reads, corresponding to ~1 Gbp of sequence. An assembly based on paired ends produced ~6.0 Mbp of genomic sequence, separated into ~19,000 contigs (mean length 312 bp), of which ~21% were fragments of putative coding sequence. The shared sequences allowed for the discovery of ~34,000 SNPs and nearly 800 indels, equivalent to a SNP frequency of 5.6 per 1,000 nt, and an indel frequency of 0.2 per 1,000 nt. A sample of heterozygous SNP loci was mapped by CAPS assays and this exercise provided validation of our mining criteria. The repetitive fraction of the genome had a high representation of retrotransposon sequence, followed by simple repeats, AT-low complexity regions and mobile DNA elements. The genomic k-mers distribution and CpG rate of <italic>C. cardunculus</italic>
, compared with data derived from three whole genome-sequenced dicots species, provided a further evidence of the random representation of the <italic>C. cardunculus </italic>
genome generated by RAD sampling.</p>
</sec>
<sec><title>Conclusion</title>
<p>The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Italie</li>
</country>
</list>
<tree><noCountry><name sortKey="Knapp, Steven J" sort="Knapp, Steven J" uniqKey="Knapp S" first="Steven J" last="Knapp">Steven J. Knapp</name>
</noCountry>
<country name="Italie"><noRegion><name sortKey="Scaglione, Davide" sort="Scaglione, Davide" uniqKey="Scaglione D" first="Davide" last="Scaglione">Davide Scaglione</name>
</noRegion>
<name sortKey="Acquadro, Alberto" sort="Acquadro, Alberto" uniqKey="Acquadro A" first="Alberto" last="Acquadro">Alberto Acquadro</name>
<name sortKey="Lanteri, Sergio" sort="Lanteri, Sergio" uniqKey="Lanteri S" first="Sergio" last="Lanteri">Sergio Lanteri</name>
<name sortKey="Portis, Ezio" sort="Portis, Ezio" uniqKey="Portis E" first="Ezio" last="Portis">Ezio Portis</name>
<name sortKey="Tirone, Matteo" sort="Tirone, Matteo" uniqKey="Tirone M" first="Matteo" last="Tirone">Matteo Tirone</name>
</country>
</tree>
</affiliations>
</record>
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