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

Abstract

The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made 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 the eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified 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 analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae)

“…To date, vast comparative chloroplast genomic studies have been conducted in a wide range of taxonomic levels, such as order (such as Dipsacales [56] and Saxifragales [57]), family (such as Orchidaceae [58] and Zingiberaceae [59]), and genus (such as Camellia [60], Lindera [61], Gossypium [62], and Ficus [17,51,63]). However, less research has focused on the comparative genomics of taxa undergoing recent speciation, such as the species complex [29].…”

“…However, other studies of comparative chloroplast genomics in Ficus identified entirely different hyper-variable intergenic regions. For example, Xia et al [63] identified trnS-GCU-trnG-UCC, trnT-GGU-psbD, trnV-UAC-trnM-CAU, clpP-…”

Analysis of the Chloroplast Genome of Ficus simplicissima Lour Collected in Vietnam and Proposed Barcodes for Identifying Ficus Plants

“…Recently, Huang et al (2022) evaluated the cp genomes of ten species in the Ficus genus. The results showed that Morus and Ficus had a close relationship compared to other genera of the Moraceae family with high bootstrap values [13,55]. In this study, the phylogenetic relationships by ML analyses were constructed based on two approaches, the complete cp genome sequence and the psbA-trnH intergenic spacer region.…”