Nuclear phylogeny of Citrus and four related genera

Despite considerable differences in morphology, the genera representing “true citrus fruit trees” are sexuallycompatible, but their phylogenetic relationships remain unclear. Most of the important commercial species of Citrus are believed to be of interspecific origin. By studying SNP and InDel polymorphisms of 27 nucleargenes on 45 genotypes of Citrus and related taxa, the average molecular differentiation between specieswas estimated, and the phylogenetic relationship between “true citrus fruit trees” was clarified. A total of16238 bp of DNA was sequenced for each genotype, and 1097 SNPs and 50 InDels were identified. Nuclearphylogenetic analysis revealed that Citrus reticulata and Fortunella form a clade clearly differentiated fromthe other two basic taxa of cultivated citrus (Citrus maxima, Citrus medica). A few genes displayed positiveselection patterns within or between species, but most of them displayed neutral patterns. The phylogeneticinheritance patterns of the analysed genes were inferred for commercial Citrus species. The SNPs and InDelsidentified are potentially very useful for the analysis of interspecific genetic structures. The nuclear phylogenyof Citrus and its sexually compatible relatives was consistent with their geographic origin. The positiveselection observed for a few genes will orient further work to analyze the molecular basis of the variability ofthe associated traits. This study presents new insights into the origin of Citrus sinensis.