Abstract
Main conclusion
The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family.
Abstract
Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88–89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.
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Data availability
The chloroplast genome sequence data of S. kouitchensis are openly available in NCBI at the GenBank database with accession number OM617848 (https://www.ncbi.nlm.nih.gov). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA726216; SAMN18926109; SRR14415465, respectively. Additional data are provided as supporting information in the online version of this article.
Abbreviations
- LSC:
-
Large single copy
- SSC:
-
Small single copy
- IR:
-
Inverted repeat
- PCGs:
-
Protein-coding genes
- SSR:
-
Simple sequence repeat
- NADH:
-
Nicotinamide adenine dinucleotide
- ATP:
-
Adenosine triphosphate
- DNA:
-
Deoxyribonucleic acid
- cpDNA:
-
Chloroplast DNA
- NCBI:
-
National Center for Biotechnology Information
- IGS:
-
Intergenic spacer
- CDS:
-
Coding sequence
- NCR:
-
Non-coding region
- MISA:
-
MicroSatellite identification tool
- TRF:
-
Tandem repeat finder
- LRT:
-
Likelihood ratio test
- ML:
-
Maximum likelihood
- RSCU:
-
Relative synonymous codon usage
- CAI:
-
Codon adaptation index
- CBI:
-
Codon bias index
- MAFFT:
-
Multiple sequence alignment program
- ANK6:
-
Ankyrin repeat protein
- MEGA:
-
Molecular evolutionary genetics analysis
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Acknowledgements
This work was supported by funds from the National Science &Technology Fundamental Resources Investigation Program of China [2018FY100705], Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences (CIFMS) [2021-I2M-1-022], National Science Foundation [81872966], Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau [2020-ZJ-Y20], Hunan technological innovation guidance project (2018SK52001). The funders were not involved in the study design, data collection, and analysis, decision to publish, or manuscript preparation. We would like to thank Miss. Jing Zen, Junchen Zhou, and Yufang Ma have provided support in arranging the basic data.
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Du, Q., Li, J., Wang, L. et al. Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family. Planta 256, 73 (2022). https://doi.org/10.1007/s00425-022-03987-z
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DOI: https://doi.org/10.1007/s00425-022-03987-z