title: A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus.
abstract: 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.
authors: Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
authors: Jose
authors: J
authors: Carbonell-Caballero
authors: Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
authors: Roberto
authors: R
authors: Alonso
authors: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
authors: Victoria
authors: V
authors: Ibañez
authors: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
authors: Javier
authors: J
authors: Terol
authors: Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
authors: Manuel
authors: M
authors: Talon
authors: Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, Valencia, Spain jdopazo@cipf.es.
authors: Joaquin
authors: J
authors: Dopazo
mesh_terms: D002957:Citrus / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics*; D054628:Genome, Chloroplast / Q000502:physiology*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D018742:DNA, Chloroplast
keywords: chloroplast genome; citrus; heteroplasmy; phylogeny; selection