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Bupleurum giraldii (H. Wolff) Koso-Pol. is a perennial herbaceous plant belonging to the Bupleurum L. (Apiaceae). It is recognized as a provincially protected rare medicinal plant in Shaanxi with the whole plant has acknowledged medicinal value. In this study, the complete plastid genome sequence of B. giraldii was sequenced and characterized, and comparative and phylogenetic analyses were then conducted alongside other published Bupleurum plastid genome sequences. The whole plastid genome of B. giraldii was 155 761 bp in length, which exhibited the conserved circular quadripartite structure consisting of a large single copy (LSC, 85 663 bp), a small single copy (SSC, 17 492 bp), and a pair of inverted repeats (IRa/IRb, 26 303 bp). A total of 129 genes were annotated, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, of which, 6 protein-coding genes, 7 tRNA genes and 4 rRNA genes were duplicated in the IR regions. A total of 66 simple sequence repeats (SSRs), 34 tandem repeats, and 31 dispersed repeats were detected. In the plastid genome of B. giraldii, codons with the relative synonymous codon usage (RSCU) value greater than 1 showed a tendency to end in adenine (A) or thymine (T), whereas those with an RSCU value less than 1 tended to end in cytosine (C) or guanine (G). Collectively, neutral plotting, ENC-plot, and PR2-plot analyses all revealed that natural selection might be the predominant factor shaping this codon usage bias. The plastid genome of Bupleurum species exhibited highly conserved gene order and content, along with little variation in overall size and GC content, no significant expansion or contraction of the IR regions was detected. Interspecific sequence variation mainly occurred in the non-coding intergenic regions, and sequence divergence in the LSC and SSC regions was significantly higher than that in the IR regions. Eleven divergence hotspot sequences were identified, located in the LSC and SSC regions respectively. Phylogenetic inferences inferred that all Bupleurum species clustered into a monophyletic clade with BSML = 100%, PP = 1, and which could be further divided into two independent lineages corresponding to subgenus Bupleurum and subgenus Penninervia. Bupleurum giraldii located in subgenus Bupleurum and showed the closest relationship to B. falcatum L. The complete plastid genome of B. giraldii was comprehensively investigated for the first time and its phylogenetic position in Bupleurum was elucidated with high resolution in this study, these results will provide basis for the conservation and sustainable utilization of the germplasm resources of medicinal Bupleurum species.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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