Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae
Identifieur interne : 000726 ( Main/Exploration ); précédent : 000725; suivant : 000727Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae
Auteurs : Pasquale L. Curci [Italie] ; Domenico De Paola [Italie] ; Donatella Danzi [Italie] ; Giovanni G. Vendramin [Italie] ; Gabriella Sonnante [Italie]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the
Url:
DOI: 10.1371/journal.pone.0120589
PubMed: 25774672
PubMed Central: 4361619
Affiliations:
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Curci</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="De Paola, Domenico" sort="De Paola, Domenico" uniqKey="De Paola D" first="Domenico" last="De Paola">Domenico De Paola</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="Danzi, Donatella" sort="Danzi, Donatella" uniqKey="Danzi D" first="Donatella" last="Danzi">Donatella Danzi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="Vendramin, Giovanni G" sort="Vendramin, Giovanni G" uniqKey="Vendramin G" first="Giovanni G." last="Vendramin">Giovanni G. Vendramin</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI)</wicri:regionArea><wicri:noRegion>Sesto Fiorentino (FI)</wicri:noRegion></affiliation></author><author><name sortKey="Sonnante, Gabriella" sort="Sonnante, Gabriella" uniqKey="Sonnante G" first="Gabriella" last="Sonnante">Gabriella Sonnante</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25774672</idno><idno type="pmc">4361619</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361619</idno><idno type="RBID">PMC:4361619</idno><idno type="doi">10.1371/journal.pone.0120589</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000129</idno><idno type="wicri:Area/Pmc/Curation">000129</idno><idno type="wicri:Area/Pmc/Checkpoint">000563</idno><idno type="wicri:Area/Ncbi/Merge">001A40</idno><idno type="wicri:Area/Ncbi/Curation">001A40</idno><idno type="wicri:Area/Ncbi/Checkpoint">001A40</idno><idno type="wicri:Area/Main/Merge">000726</idno><idno type="wicri:Area/Main/Curation">000726</idno><idno type="wicri:Area/Main/Exploration">000726</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae</title><author><name sortKey="Curci, Pasquale L" sort="Curci, Pasquale L" uniqKey="Curci P" first="Pasquale L." last="Curci">Pasquale L. Curci</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="De Paola, Domenico" sort="De Paola, Domenico" uniqKey="De Paola D" first="Domenico" last="De Paola">Domenico De Paola</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="Danzi, Donatella" sort="Danzi, Donatella" uniqKey="Danzi D" first="Donatella" last="Danzi">Donatella Danzi</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author><author><name sortKey="Vendramin, Giovanni G" sort="Vendramin, Giovanni G" uniqKey="Vendramin G" first="Giovanni G." last="Vendramin">Giovanni G. Vendramin</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI)</wicri:regionArea><wicri:noRegion>Sesto Fiorentino (FI)</wicri:noRegion></affiliation></author><author><name sortKey="Sonnante, Gabriella" sort="Sonnante, Gabriella" uniqKey="Sonnante G" first="Gabriella" last="Sonnante">Gabriella Sonnante</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Institute of Biosciences and Bioresources, National Research Council, Bari, Italy</addr-line></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea>Institute of Biosciences and Bioresources, National Research Council, Bari</wicri:regionArea><wicri:noRegion>Bari</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the <italic>ndhF</italic> gene generating an overlap between the <italic>ndhF</italic> and <italic>ycf1</italic> genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the <italic>Cynara</italic> genus. Parsimony-informative regions were evaluated and allowed to place a <italic>Cynara</italic> species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for “specific barcode” purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bremer, K" uniqKey="Bremer K">K Bremer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rottenberg, A" uniqKey="Rottenberg A">A Rottenberg</name></author><author><name sortKey="Zohary, D" uniqKey="Zohary D">D Zohary</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sonnante, G" uniqKey="Sonnante G">G Sonnante</name></author><author><name sortKey="Pignone, D" uniqKey="Pignone D">D Pignone</name></author><author><name sortKey="Hammer, K" uniqKey="Hammer K">K Hammer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gebhardt, R" uniqKey="Gebhardt R">R 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Erickson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ortiz, S" uniqKey="Ortiz S">S Ortiz</name></author><author><name sortKey="Bonifacino, Jm" uniqKey="Bonifacino J">JM Bonifacino</name></author><author><name sortKey="Crisci, Jv" uniqKey="Crisci J">JV Crisci</name></author><author><name sortKey="Funk, Va" uniqKey="Funk V">VA Funk</name></author><author><name sortKey="Hansen, Hv" uniqKey="Hansen H">HV Hansen</name></author><author><name sortKey="Hind, Djn" uniqKey="Hind D">DJN Hind</name></author><author><name sortKey="Funk, Va" uniqKey="Funk V">VA Funk</name></author><author><name sortKey="Susanna, A" uniqKey="Susanna A">A Susanna</name></author><author><name sortKey="Stuessy, Tf" uniqKey="Stuessy T">TF Stuessy</name></author><author><name sortKey="Bayer, Rj" uniqKey="Bayer R">RJ Bayer</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Italie</li></country></list><tree><country name="Italie"><noRegion><name sortKey="Curci, Pasquale L" sort="Curci, Pasquale L" uniqKey="Curci P" first="Pasquale L." last="Curci">Pasquale L. Curci</name></noRegion><name sortKey="Danzi, Donatella" sort="Danzi, Donatella" uniqKey="Danzi D" first="Donatella" last="Danzi">Donatella Danzi</name><name sortKey="De Paola, Domenico" sort="De Paola, Domenico" uniqKey="De Paola D" first="Domenico" last="De Paola">Domenico De Paola</name><name sortKey="Sonnante, Gabriella" sort="Sonnante, Gabriella" uniqKey="Sonnante G" first="Gabriella" last="Sonnante">Gabriella Sonnante</name><name sortKey="Vendramin, Giovanni G" sort="Vendramin, Giovanni G" uniqKey="Vendramin G" first="Giovanni G." last="Vendramin">Giovanni G. Vendramin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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