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

Abstract

AbstractBackgroundFerulaL. 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 ofFerulaand its neighboring generaSoranthusLedeb.,SchumanniaKuntze., andTalassiaKorovin, we sequenced 14 complete plastomes of 12 species. ResultsThe 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, andTalassiashould be considered synonymous withFerula. Six highly divergent regions (rps16/trnQ-UUG,trnS-UGA/psbZ,psbH/petB,ycf1/ndhF,rpl32, andycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection geneccsAmay be a discriminating DNA barcode forFerulaspecies.ConclusionPlastids 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 ofFerula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.