Phylogenetic patterns and molecular evolution among ‘True citrus fruit trees’ group (Rutaceae family and Aurantioideae subfamily)

Abstract

Cytoplasmic chloroplast DNAs was explored to establish phylogenetic relationships among ‘True citrus’ group and elucidate its molecular evolution. Conserved group I intron (PQRS) sequence motifs were detected in Citrus genus and showed differences of nucleotide variation between elements and some species. The P8 stem-loop region was the only variable region in trnL intron of Citrus species. The deletion of 6 bp has been detected between sites (40–45) in the partial alignment of P8 stem-loop resulted in a change in conformation of the secondary structures in the ancestral species and other derived species and this could be explained by the evolution and speciation of this genus. The consistency index (CI=1) and the retention index (RI=1) values suggest that the changes are mostly apomorphic despite the absence of homoplasy (HI=0). The phylogenetic tree confirms and shows a branching of C. limon, C. sinensis, C. paradisi, C. tangelo and C. aurantium in a monophyletic clade. This result so far to C. reticulata ruled out the maternal contribution of mandarin gene pool in the elaboration of these secondary Citrus species. The Maximum Likelihood tree indicated that the genus Citrus is quite distant from the related genera Poncirus, Microcitrus, Eremocitrus and Fortunella except only Fortunella margarita species. Here new insight is given about mechanism involving in the evolution of the trnL intron in ‘True Citrus’. From the study it appears that an explicit rejection of the null hypothesis and a scenario of a demography history and recent expansion of ‘True Citrus’ genotypes seem to be retained that may be an important factor influencing the power of genetic diversity in ‘True Citrus’.