TY - JOUR T1 - A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. JF - Molecular biology and evolution Y1 - 2015 A1 - Carbonell-Caballero, José A1 - Alonso, Roberto A1 - Ibañez, Victoria A1 - Terol, Javier A1 - Talon, Manuel A1 - Dopazo, Joaquin KW - chloroplast KW - citrus KW - Phylogeny KW - WGS AB - 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 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 analysed 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. VL - 32 UR - http://mbe.oxfordjournals.org/content/early/2015/04/27/molbev.msv082.full ER -