Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L

Abstract

Background: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species.

Conclusion: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Keywords: Chloroplast genome; Comparative analysis; Ferula; Phylogenetic relationships.

Fig. 1

Chloroplast genome maps for Ferula L. Genes on the inside of the circle are transcribed clockwise and those on the outside are transcribed counterclockwise. The darker gray inner circle corresponds to the GC content, whereas the lighter gray indicates the AT content. Different colors represent different functional genes

Fig. 2

Relative synonymous codon usage (RSCU) values of all merged protein-coding genes for 14 Ferula plastomes. Color key: red values indicate higher RSCU values, and blue values indicate lower RSCU values. M = initiation codon, * = termination codon, I = l-isoleucine codon, and V = Valine codon

Fig. 3

Comparison of the border regions of the 14 studied Ferula plastomes

Fig. 4

Sequence identity plots of the newly sequenced chloroplast genomes

Fig. 5

Sliding window analysis of the newly sequenced chloroplast genomes of Ferula species

Fig. 6

a Branch length diagram of the phylogenetic tree. b Phylogenetic tree of the 25 species inferred from maximum likelihood (ML) and Bayesian inference (BI) analyses based on the complete plastomes. The Shimodaira-Hasegawa-like support values approximate the likelihood ratio test (only F. oopoda and F. gigantea had SH-aLRT values below 80 in the terminal branch), and ultrafast bootstrap values (UFBS ≥ 95%, on the right) are shown on the branches. Green indicates two sequences of S. meyeri (F. sibiraca), blue indicates one sequence of S. karelinii (F. karelinii), and red indicates two sequences of T. transiliensis (F. transiliensis)