Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 32, Issue 8, Pages 2015-2035Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msv082
Keywords
chloroplast genome; citrus; phylogeny; heteroplasmy; selection
Funding
- Citruseq-Citrusgenn Consortium
- Ministerio de Ciencia e Innovacion through FEDER [PSE-060000-2009-8, IPT-010000-2010-43]
- Spanish Ministry of Economy and Competitiveness (MINECO) [BIO2011-27069]
- Conselleria de Educacio of the Valencia Community [PROMETEOII/2014/025]
- National Institute of Bioinformatics
- initiative of the Instituto de Salud Carlos III (ISCIII)
- Bull S.A. through the Bull Chair in Computational Genomics
- [AGL2011-30240]
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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.
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