Abstract
Carpesium abrotanoides L. is a widely used medicinal plant in China belonging to the tribe Inuleae of Family Asteraceae. Here, we determined the complete chloroplast (cp) genome sequence of C. abrotanoides and conducted a comparative analysis with closely related species from tribe Inuleae. The cp genome of C. abrotanoides exhibited a typical quadripartite structure with a full length of 151,394 bp, containing a total number of 133 genes. The gene order and GC content were highly consistent in the Inuleae plants according to the comparative analysis results. The number of potential RNA editing sites in 20 protein-coding genes of Inuleae species ranged from 43 in Inula hupehensis to 51 in Inula racemosa. In addition, 41 SSRs and 40 long repeats have been identified in the cp genomes of C. abrotanoides, exhibiting significant differences with that from other Inuleae plants. Six potential hotspots with high Pi values were identified among C. abrotanoides and other Inuleae species, including three intergenic spacer regions, two tRNA regions and one protein-coding region(ycf1). Furthermore, five pairs of primers targeting the divergence regions were accordingly designed, providing potential molecular markers for population genetic investigations in Inuleae species. The phylogenetic analysis based on conserved chloroplast protein coding genes revealed a sister relationship between C. abrotanoides and three Inula species with strong bootstrap support, indicating a close relationship between the two genera. This study enhanced the understanding of the evolution of Carpesium within the tribe Inuleae, identified several nucleotide diversity hotspots and provided the comparative information on the chloroplast genome, which could contribute to the molecular species discrimination and phylogenetic studies of Inuleae plants.
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Abbreviations
- LSC:
-
Large single copy
- SSC:
-
Small single copy
- IR:
-
Inverted repeat regions
- MAFFT:
-
Multiple Alignment using Fast Fourier Transform
- RSCU:
-
Relative synonymous codon usage
- Ks:
-
Synonymous substitution
- Ka:
-
Non-synonymous substitutions
- SNPs:
-
Single nucleotide polymorphisms
- InDels:
-
Insertions and deletions
- Ts:
-
Transitions substitutions
- Tv:
-
Transversion substitutions
- Ts/Tv:
-
Ratio of transition to transversion substitutions
- SSR:
-
Simple sequence repeats
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Acknowledgements
We thank Shuisheng Yu and Yuqing Ge for their assistance and helpful suggestions during work. This work was financially supported by the Opening Project of Zhejiang Provincial Preponderant and Characteristic Subject of Key University (Traditional Chinese Pharmacology) Zhejiang Chinese Medical University (No. ZYAOX2018033).
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All authors contributed to the study conception and design. XH, CG and RC designed the experiments and organized the manuscript. RC and QW collected the samples of Carpesium abrotanoides. XH, SD and MZ performed the experiments and conduced the comparative analysis. XH, SD and CG wrote the manuscript. RC was involved in writing-review and funding acquisition. All authors read and approved the final manuscript.
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He, X., Dong, S., Gao, C. et al. The complete chloroplast genome of Carpesium abrotanoides L. (Asteraceae): structural organization, comparative analysis, mutational hotspots and phylogenetic implications within the tribe Inuleae. Biologia 77, 1861–1876 (2022). https://doi.org/10.1007/s11756-022-01038-2
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DOI: https://doi.org/10.1007/s11756-022-01038-2