New insights on limes and lemons origin from targeted nuclear gene sequencing and cytoplasmic marker

It is believed that Citrus medica, Citrus maxima, Citrus reticulata and Citrus micrantha have generated allcultivated Citrus species. Depending on the classification, lemons and limes are classified either into twospecies, Citrus limon and Citrus aurantifolia (Swingle and Reece) or into more than 30 (Tanaka). In order tostudy the molecular phylogeny of this Citrus group, we analyzed 20 targeted sequenced nuclear genes andused 3 mitochondrial and 3 chloroplastic markers for 21 lemons and limes compared with representatives ofthe 4 basic taxa. We observed 3 main groups, each one derived from direct interspecific hybridizations: (1)the Mexican lime group (C. aurantifolia), including Citrus macrophylla, arising from hybridization betweenpapeda (C. micrantha) and citron (C. medica); (2) the yellow lemon group (C. limon) that are hybrids betweensour orange (Citrus aurantium, which is believed to be a hybrid between C. maxima and C. reticulata) andcitron; and (3) a rootstock lemon/lime group (Rough lemon and Rangpur lime) that are hybrids betweenthe acid small mandarin group and citron. We also identified different probable backcrosses and genotypeswith more complex origins. None of the analyzed limes and lemons shared the C. medica cytoplasm, whilethis taxon is the common nuclear contributor of all limes and lemons. Limes and lemons appear to be a verycomplex citrus varietal group with the contribution of the 4 basic taxa. Neither the Swingle and Reece nor theTanaka classifications fit with the genetic evidence.