Carbonell-Caballero Jose, Alonso Roberto, Ibañez Victoria, Terol Javier, Talon Manuel, Dopazo Joaquin
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain.
Mol Biol Evol. 2015 Aug;32(8):2015-35. doi: 10.1093/molbev/msv082. Epub 2015 Apr 14.
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.
柑橘属包含一些全球最重要的栽培果树。尽管因其商业价值受到广泛研究，但栽培柑橘品种的起源及其驯化历史仍是一个悬而未决的问题。在此，我们对34个柑橘基因型的叶绿体基因组进行了系统发育分析，这是迄今为止关于柑橘属进化和变异性最全面、最详细的研究。使用统计模型来估计主要柑橘类群之间的分歧时间。此外，还绘制了不同柑橘物种基因组变异的完整图谱，包括单核苷酸变异、异质性位点、插入缺失（插入和缺失）以及大的结构变异。所有这些变异的分布为所得系统发育提供了进一步的独立支持。一个意外发现是在几个分析的基因组中发现了高水平的异质性。完整叶绿体DNA的使用不仅为更好地理解柑橘属内的系统发育关系铺平了道路，还为其他难以捉摸的进化过程，如叶绿体遗传、异质性和基因选择，提供了独到见解。
