A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus
Identifieur interne : 000824 ( Main/Exploration ); précédent : 000823; suivant : 000825A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus
Auteurs : Jose Carbonell-Caballero [Espagne] ; Roberto Alonso [Espagne] ; Victoria Iba Ez [Espagne] ; Javier Terol [Espagne] ; Manuel Talon [Espagne] ; Joaquin Dopazo [Espagne]Source :
- Molecular Biology and Evolution [ 0737-4038 ] ; 2015.
Abstract
Url:
DOI: 10.1093/molbev/msv082
PubMed: 25873589
PubMed Central: 4833069
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus <italic>Citrus</italic></title><author><name sortKey="Carbonell Caballero, Jose" sort="Carbonell Caballero, Jose" uniqKey="Carbonell Caballero J" first="Jose" last="Carbonell-Caballero">Jose Carbonell-Caballero</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Alonso, Roberto" sort="Alonso, Roberto" uniqKey="Alonso R" first="Roberto" last="Alonso">Roberto Alonso</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Iba Ez, Victoria" sort="Iba Ez, Victoria" uniqKey="Iba Ez V" first="Victoria" last="Iba Ez">Victoria Iba Ez</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Dopazo, Joaquin" sort="Dopazo, Joaquin" uniqKey="Dopazo J" first="Joaquin" last="Dopazo">Joaquin Dopazo</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="msv082-AFF3">Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25873589</idno><idno type="pmc">4833069</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833069</idno><idno type="RBID">PMC:4833069</idno><idno type="doi">10.1093/molbev/msv082</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000363</idno><idno type="wicri:Area/Pmc/Curation">000362</idno><idno type="wicri:Area/Pmc/Checkpoint">000630</idno><idno type="wicri:Area/Ncbi/Merge">001A84</idno><idno type="wicri:Area/Ncbi/Curation">001A84</idno><idno type="wicri:Area/Ncbi/Checkpoint">001A84</idno><idno type="wicri:doubleKey">0737-4038:2015:Carbonell Caballero J:a:phylogenetic:analysis</idno><idno type="wicri:Area/Main/Merge">000824</idno><idno type="wicri:Area/Main/Curation">000824</idno><idno type="wicri:Area/Main/Exploration">000824</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus <italic>Citrus</italic></title><author><name sortKey="Carbonell Caballero, Jose" sort="Carbonell Caballero, Jose" uniqKey="Carbonell Caballero J" first="Jose" last="Carbonell-Caballero">Jose Carbonell-Caballero</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Alonso, Roberto" sort="Alonso, Roberto" uniqKey="Alonso R" first="Roberto" last="Alonso">Roberto Alonso</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Iba Ez, Victoria" sort="Iba Ez, Victoria" uniqKey="Iba Ez V" first="Victoria" last="Iba Ez">Victoria Iba Ez</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF2">Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Dopazo, Joaquin" sort="Dopazo, Joaquin" uniqKey="Dopazo J" first="Joaquin" last="Dopazo">Joaquin Dopazo</name><affiliation wicri:level="1"><nlm:aff id="msv082-AFF1">Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="msv082-AFF3">Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular Biology and Evolution</title><idno type="ISSN">0737-4038</idno><idno type="eISSN">1537-1719</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><italic>Citrus</italic> genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here, we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus <italic>Citrus</italic>. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels (insertions and deletions), and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analyzed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the <italic>Citrus</italic> genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Akaike, H" uniqKey="Akaike H">H Akaike</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Araujo, E" uniqKey="Araujo 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uniqKey="Dopazo J" first="Joaquin" last="Dopazo">Joaquin Dopazo</name><name sortKey="Dopazo, Joaquin" sort="Dopazo, Joaquin" uniqKey="Dopazo J" first="Joaquin" last="Dopazo">Joaquin Dopazo</name><name sortKey="Iba Ez, Victoria" sort="Iba Ez, Victoria" uniqKey="Iba Ez V" first="Victoria" last="Iba Ez">Victoria Iba Ez</name><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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