A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus Jose Carbonell-Caballero,1 Roberto Alonso,1 Victoria Ibanez,~ 2 Javier Terol,2 Manuel Talon,2 and Joaquin Dopazo*,1,3 1Computational Genomics Department, Centro de Investigacion Prıncipe Felipe (CIPF), Valencia, Spain 2Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain 3Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain *Corresponding author: E-mail:
[email protected]. Associate editor: Shizhong Xu Abstract Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied Downloaded from 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, hetero- http://mbe.oxfordjournals.org/ plasmic 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 hetero- plasmy 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.