Comparative Analysis of Complete Chloroplast Genomes of Eight Ficus Species and Insights Into Phylogenetic Relationships of Ficus

Abstract

Background The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and often used as food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years. Results In this study, the eight Ficus species (Ficus altissima, F. auriculata, F. benjamina, F. curtipes, F. heteromorpha, F. lyrata, F. microcarpa, and F. virens) complete chloroplast(cp) genomes were successfully sequenced and phylogenetic analyses with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC and ycf1). Phylogenetic analysis showed that three subgen. (Sycomorus, Ficus. Pharmacosycea) of Ficus as monophyletic, but Urostigma is no-monophyletic. Conclusions In our study, we have successfully assembled and analysed the cp genomes of eight Ficus species. The results give useful data for further studies on molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus.