Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species

Abstract

Background The large genus Ficus comprises approximately 800 species, most of which possess high ornamental and ecological values. However, its evolutionary history remains largely unknown. Plastome (chloroplast genome) analysis had become an essential tool for species identification and for unveiling evolutionary relationships between species, genus and other rank groups. In this work we present the plastomes of ten Ficus species. Results The complete chloroplast (CP) genomes of eleven Ficus specimens belonging to ten species were determined and analysed. The full length of the Ficus plastome was nearly 160 kbp with a similar overall GC content, ranging from 35.88 to 36.02%. A total of 114 unique genes, distributed in 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, were annotated in each of the Ficus CP genome. In addition, these CP genomes showed variation in their inverted repeat regions (IR). Tandem repeats and mononucleotide simple sequence repeat (SSR) are widely distributed across the Ficus CP genome. Comparative genome analysis showed low sequence variability. In addition, eight variable regions to be used as potential molecular markers were proposed for future Ficus species identification. According to the phylogenetic analysis, these ten Ficus species were clustered together and further divided into three clades based on different subgenera. Simultaneously, it also showed the relatedness between Ficus and Morus. Conclusion The chloroplast genome structure of 10 Ficus species was similar to that of other angiosperms, with a typical four-part structure. Chloroplast genome sizes vary slightly due to expansion and contraction of the IR region. And the variation of noncoding regions of the chloroplast genome is larger than that of coding regions. Phylogenetic analysis showed that these eleven sampled CP genomes were divided into three clades, clustered with species from subgenus Urostigma, Sycomorus, and Ficus, respectively. These results support the Berg classification system, in which the subgenus Ficus was further decomposed into the subgenus Sycomorus. In general, the sequencing and analysis of Ficus plastomes, especially the ones of species with no or limited sequences available yet, contribute to the study of genetic diversity and species evolution of Ficus, while providing useful information for taxonomic and phylogenetic studies of Ficus.

Analysis of Michelia（Magnoliaceae）chloroplast genomes: Provide New Insights into Intergeneric and Intrageneric Relationships

“…The six cp genomes of the genus Michelia ranged in size from 159,703 to 160,026 bp, with an average GC content of 39.26% and codon usage mostly ending in A/U, similar to the other cp genomes of Magnoliaceae, indicating that higher plants have a stable genome structure [5,[24][25][26]. In this study, the transfer of the gene rpl2 to the LSC region resulted in a shorter IR region and a longer LSC region in M. doltsopa, and this gene transfer is also present in a variety of angiosperms [25,[27][28][29]. This suggested that the conservation of cp genome sequences in higher plants coexists with IR boundary diversity, which in turn ensures genome diversity [14,[30][31][32].…”

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

“…In this study, we implemented a comprehensive comparative analysis of 22 plastomes from Ferula , Talassia , and Soranthus . All plastomes possessed a typical circular tetrad structure with two inverted repeat regions, one SSC region, and one LSC region, which is common in other plants [ 44 – 46 ]. Additionally, the gene numbers, type and distribution of large repeats, number and type of SSRs, and codon usage were rather similar among these plastomes.…”

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].…”

“…The 13 F. sarmentosa complex chloroplast genomes were combined with 36 Ficus chloroplast genomes from GenBank and 59 Ficus genomes published by Bruun-Lund et al [26]. Additionally, 18 genomes from the China National GeneBank (accession number: CNP0001337) and Genome Sequence Archive (accession number: PRJCA002187) [15,51], including 8 samples belonging to the F. sarmentosa complex, were assembled to further explore the Ficus phylogenomics and the potential of chloroplast genomes to resolve the evolutionary relationships among the closely related species. Seven samples from the Olmedieae tribe were chosen as the outgroup, according to previous studies [26,52].…”