A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus
Citrus 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 analys...
| Autores principales: | , , , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2017
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| Acceso en línea: | http://hdl.handle.net/20.500.11939/4965 https://academic.oup.com/mbe/article/32/8/2015/2925553 |
| _version_ | 1855032203872829440 |
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| author | Carbonell-Caballero, Jose Alonso, Roberto Ibanez, Victoria Terol, Javier Talón, Manuel Dopazo, Joaquín |
| author_browse | Alonso, Roberto Carbonell-Caballero, Jose Dopazo, Joaquín Ibanez, Victoria Talón, Manuel Terol, Javier |
| author_facet | Carbonell-Caballero, Jose Alonso, Roberto Ibanez, Victoria Terol, Javier Talón, Manuel Dopazo, Joaquín |
| author_sort | Carbonell-Caballero, Jose |
| collection | ReDivia |
| description | Citrus 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 Citrus. 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 Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection. |
| format | article |
| id | ReDivia4965 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia49652025-04-25T14:45:02Z A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus Carbonell-Caballero, Jose Alonso, Roberto Ibanez, Victoria Terol, Javier Talón, Manuel Dopazo, Joaquín Citrus 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 Citrus. 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 Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection. 2017-06-01T10:11:27Z 2017-06-01T10:11:27Z 2015 AUG 2015 article publishedVersion Carbonell-Caballero, J., Alonso, Roberto, Ibanez, Victoria, Terol, J., Talon, M., Dopazo, J. (2015). A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Molecular biology and evolution, 32(8), 2015-2035. 0737-4038 http://hdl.handle.net/20.500.11939/4965 10.1093/molbev/msv082 https://academic.oup.com/mbe/article/32/8/2015/2925553 en openAccess Impreso |
| spellingShingle | Carbonell-Caballero, Jose Alonso, Roberto Ibanez, Victoria Terol, Javier Talón, Manuel Dopazo, Joaquín A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title | A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title_full | A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title_fullStr | A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title_full_unstemmed | A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title_short | A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus |
| title_sort | phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus citrus |
| url | http://hdl.handle.net/20.500.11939/4965 https://academic.oup.com/mbe/article/32/8/2015/2925553 |
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