Investigation of the phylogenetic relationships within the genus Citrus (Rutaceae) and related species in Korea using plastid trnL-trnF sequences

The phylogenetic relationships within the genus Citrus and related species found in Korea were analyzed by comparing the trnL-trnF intergenic spacer sequences of the chloroplast DNA (cpDNA). All 21 accessions had trnL-trnF sequences of identical length, 372 base pairs (bp). Of the 377 aligned positions in the trnL-trnF regions of these species, 67 sites were variable (17.8%, 67/377). Pairwise sequence divergences in the trnL-trnF region ranged from 0 to 3.2% in the ingroup accessions and from 8.8 to 10.9% between the in- and the outgroup species Phellodendron amurense. The greatest divergence (3.2%) was between C. aurantium and C. natsudaidai. A phylogenetic tree was generated based on maximum parsimony (MP) analysis of the trnL-trnF sequences data from 22 accessions, including the outgroup taxon, producing 17 equally most parsimonious trees. The consensus tree contained eight independent clusters. Cluster I contained C. platymamma, which has a collared fruit shape, unique among Korean Citrus. Cluster II contained mostly mandarin and pummelo accessions. Cluster V contained C. sunki and six accessions of C. unshiu. Four of six C. unshiu accessions had identical sequences. In addition, Nagami kumquat (Fortunella margarita) was phylogenetically close to Citrus, whereas the trifoliate orange (Poncirus trifoliate) was distant from Korean Citrus species, both local species and cultivars. These results confirmed that analyses of cpDNA trnL-trnF sequences can detect enough polymorphisms to differentiate Korean Citrus species and to determine their phylogenetic relationships.