Abstract
Vicatia thibetica de Boiss.: a herb in the family Apiaceae, has been used for over a hundred years as an essential medicinal and edible plant in the Bai ethnic group of Dali City. However, due to the lack of study on plastid genomes of V. thibetica, studies of comparison and phylogeny with other related species remain scarce. In the current study, we assembled, annotated, and characterized the entire chloroplast (cp) genome of V. thibetica through high-throughput sequencing for the first time, compared with published whole chloroplast genomes from the same family. A phylogenetic analysis of the chloroplast genome has also been performed. The whole chloroplast genome of V. thibetica was 145,796 in size and consisted of a large single-copy region (LSC; 92,186 bp), a small single-copy region (SSC; 17,452 bp), and a pair of inverted repeat regions (IRs; 18,079 bp) forming a circular quadripartite structure. Annotation resulted in 128 genes, including 84 protein-coding genes (PCGs), 35 transfer RNA genes (tRNAs), eight ribosomal genes (rRNAs), and one pseudogene. Repeat sequence analysis displayed V. thibetica plastid genome contains 75 simple repeats, 37 long repeats, and 29 tandem repeats. Compared with the cp genome of other Apiaceae species, a common feature was that the IR regions of the genome were more conservative compared to the LSC and SSC regions. Highly variable hotspots included rps16, ndhC-trnV-UAC, clpP, ycf1, and ndhB in the genomes, which supply valuable molecular markers for phylogeny, identification, and classification in the Apiaceae family. The results of phylogenetic analysis strongly supported the genus Vicatia as an independent genus in the family Apiaceae, in which the closest affinities to the related species of Angelica, Peucedanum, and Ligusticum were observed. In conclusion, the first chloroplast genome of Vicatia reported in this study may improve our understanding of phylogenetic relationship of different genera of Apiaceae. In addition, the current data will be valuable as chloroplast genomic resource for species identification and population genetics.
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Data availability
The data that support the findings of this study are publicly available in the GenBank of the NCBI database under Accession Number MZ189732.
Abbreviations
- Cp:
-
Chloroplast
- IR:
-
Inverted repeat
- LSC:
-
Large single-copy
- SSC:
-
Small single-copy
- PCGs:
-
Protein-coding genes
- rRNAs:
-
Ribosomal RNA genes
- tRNAs:
-
Transfer RNA genes
- SSR:
-
Simple sequence repeat
- RSCU:
-
Relative synonymous codon usage
- ML:
-
Maximum likelihood
- NJ:
-
Neighbor-joining
- CDS:
-
Protein-coding regions
- IGS:
-
Intergenic spacer
References
Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34:3030–3031. https://doi.org/10.1093/bioinformatics/bty220/4961430
Asaf S, Khan AL, Khan MA (2018) Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species. PLoS ONE 13:e0192966. https://doi.org/10.1371/journal.pone.0192966
Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var “Ridge Pineapple”: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21. https://doi.org/10.1186/1471-2229-6-21
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580. https://doi.org/10.1093/nar/27.2.573
Bi Y, Zhang MF, Xue J, Dong R, Du YP, Zhang X (2018) Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep 8:397–416. https://doi.org/10.1038/s41598-018-19591-9
Biju VC, Shidhi PR, Vijayan S, Rajan VS, Sasi A, Janardhanan A, Nair AS (2019) The Complete chloroplast genome of Trichopus zeylanicus, and phylogenetic analysis with dioscoreales. Plant Genome 12(3):1–11. https://doi.org/10.3835/plantgenome2019.04.0032
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics 19(Suppl 1):i54–i62. https://doi.org/10.1093/bioinformatics/btg1005
Chen Q, Wu XB, Zhang DQ (2019) Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. Peer J 7:7e7480. https://doi.org/10.7717/peerj.7480
Dierckxsens N, Mardulyn P, Smits G (2016) NOVOPlasty:de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:e18. https://doi.org/10.1093/nar/gkw955
Dong WP, Liu J, Yu J, Wang L, Zhou SL (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7(4):e35071. https://doi.org/10.1371/journal.pone.0035071
Dong WP, Liu H, Xu C, Zuo YJ, Chen ZJ, Zhou SL (2014) A chloroplast genomic strategy for designing taxon specific DNA mini-barcodes: a case study on ginsengs. BMC Genet 15:138. https://doi.org/10.1186/s12863-014-0138-z
Dong ST, Zhang XQ, Hu Y (2018) General situation of chemical composition, quality control and pharmacology of Xigui. Chin J Ethnomed Ethnopharm 27(13):40–42
Du Y, Bi Y, Yang F, Zhang M, Chen X, Xue J, Zhang X (2017) Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses. Sci Rep 7:233–252. https://doi.org/10.1038/s41598-017-06210-2
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279. https://doi.org/10.1093/nar/gkh458
Ge L, Shen LQ, Chen QY, Li XM, Zhang L (2017) The complete chloroplast genome sequence of Hydrocotyle sibthorpioides (Apiales: araliaceae). Mitochondrial DNA Part B 2(1):29–30. https://doi.org/10.1080/23802359.2016.1241676
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41(41):95–98. https://doi.org/10.1021/bk-1999-0734.ch008
Jansen RK, Cai ZQ, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J (2007) Analysis of 81genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci 104:19369–19374. https://doi.org/10.1073/pnas
Jiang B, Zhao G, Zhang DQ (2016) An illustrated book of bai nationality medicinal plants. Chinese Medicine Press, Beijing, p 156
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. https://doi.org/10.1093/molbev/mst010
Kim KJ, Lee HL (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11(4):247–261. https://doi.org/10.1093/dnares/11.4.247
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29(22):4633–4642. https://doi.org/10.1093/nar/29.22.4633
Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29(6):1695–1701. https://doi.org/10.1093/molbev/mss020
Li YS, Geng ML, Xu ZL, Wang Q, Li LL, Xu M, Li MM (2019) The complete plastome of Peucedanum praeruptorum (Apiaceae). Mitochondrial DNA Part B 4(2):3612–3613. https://doi.org/10.1080/23802359.2019.1676180
Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52(5–6):267–274. https://doi.org/10.1007/s00294-007-0161-y
Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30(5):1188–1195. https://doi.org/10.1093/molbev/mst024
Nguyen L, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268–274. https://doi.org/10.1093/molbev/msu300
Nie XJ, Lv SZ, Zhang YX, Du XH, Wang L, Biradar SS, Tan XF, Wan FH, Weining S, Kolokotronis S (2012) Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS ONE 7(5):e36869. https://doi.org/10.1371/journal.pone.0036869
Park I, Yang S, Kim W, Song JH, Lee HS, Lee HO, Lee JH, Ahn SN, Moon BC (2019) Sequencing and comparative analysis of the chloroplast genome of Angelica polymorpha and the development of a novel indel marker for species identification. Molecules 24(6):1038. https://doi.org/10.3390/molecules24061038
Powell W, Morgante M, Andre C, McNicol JW, Machray GC, Doyle JJ, Tingey SV, Rafalski JA (1995) Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol 5(9):1023–1029. https://doi.org/10.1016/S0960-9822(95)00206-5
Pu FD, Mark FW (2005) Vicatia DC. In: Wu ZY, Hong DY, Raven PH (eds) Flora of China, vol 14. Science Press and Missouri Botanical Garden Press, Beijing and St Louis, pp 52
Pu FD (2005) Taxonomic notes on Meeboldia H. Wolff (Umbelliferae). Acta Phytotaxonomica Sinica 43(6):552. https://doi.org/10.1360/aps030076
Raven JA, Allen JF (2003) Genomics and chloroplast evolution: What did cyanobacteria do for plants? Genome Biol 4(3):209. https://doi.org/10.1186/gb-2003-4-3-209
Ren T, Li ZX, Xie DF, Gui LJ, Peng C, Wen J, He XJ (2020) Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships. BMC Plant Biol 20(1):519–519. https://doi.org/10.1186/s12870-020-02696-7
Roullier C, Rossel G, Tay D, McKey D, Lebot V (2011) Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces. Mol Ecol 20(19):3963–3977. https://doi.org/10.1111/j.1365-294X.2011.05229.x
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34(12):3299–3302. https://doi.org/10.1093/molbev/msx248
Sharp PM, Tuohy Therese MF, Mosurski Krzysztof R (1986) Codon usage in yeast: cluster analysis clearly diferentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143. https://doi.org/10.1093/nar/14.13.5125
Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288
She ML, Pu FD, Pan ZH, Mark FW (1979) Apiaceae lindley. In: Wu ZY, Hong DY, Raven PH (eds) Flora of China, vol 55. Science Press and Missouri Botanical Garden Press, Beijing and St Louis, pp 185
Tang P, Ruan QY, Peng C (2011) Phylogeny in structure alterations of poaceae cpDNA. Chin Agric Sci Bull 27:171–176
Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422. https://doi.org/10.1007/s00122-002-1031-0
Tian EW, Liu QQ, Chen WN, Li F, Chen AM, Li C, Chao Z (2019) Characterization of complete chloroplast genome of Angelica sinensis (Apiaceae), an endemic medical plant to China. Mitochondrial DNA Part B 4(1):158–159. https://doi.org/10.1080/23802359.2018.1544862
Watson MF (1998) Notes relating to the flora of Bhutan: XXXVI. Umbelliferae, II. Edinburgh J Bot 55(3):367–415. https://doi.org/10.1017/S0960428600003267
Wu QW, Wu H, Wang LK, Zhao X (2020) Characterization of the complete chloroplast genome of Ligusticum sinense, as a Chinese herb to treat toothache in China. Mitochondrial DNA Part B 5(3):3174–3175. https://doi.org/10.1080/23802359.2020.1808103
Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20(17):3252–3255. https://doi.org/10.1093/bioinformatics/bth352
Xiao QY, Feng T, Yu Y, Luo Q, He XJ (2019) The complete chloroplast genome of Semenovia gyirongensis (Tribe Tordylieae, Apiaceae). Mitochondrial DNA Part B 4(1):1863–1864. https://doi.org/10.1080/23802359.2019.1613199
Zhang W, Duan ZH, Sun F (2004) The Chemical constituents from the root of Vicatia Thibetica. Nat Prod Res Dev 16:218–219
Zhang ZL, Zhang Y, Song MF, Guan YH, Ma XJ (2019a) Species identification of Dracaena using the complete chloroplast genome as a super-barcode. Front Pharmacol 10:1441. https://doi.org/10.3389/fphar.2019.01441
Zhang F, Zhao ZY, Yuan QJ, Chen SQ, Huang LQ (2019b) The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae). Mitochondrial DNA Part B 4(2):3665–3666. https://doi.org/10.1080/23802359.2019.1678427
Zheng HY, Guo XL, He XJ, Yu Y, Zhou SD (2019) The complete chloroplast genome of Chamaesium paradoxum. Mitochondrial DNA Part B 4(1):2069–2070. https://doi.org/10.1080/23802359.2019.1617064
Zheng ZY, Li J, Xie DF, Zhou SD, He XJ (2020) The complete chloroplast genome sequence of Heracleum yungningense. Mitochondrial DNA Part B 5:1783–1784. https://doi.org/10.1080/23802359.2020.1749150
Zhou N, Duan YM, Chen Q, Ma XK (2007) Study on Pharmacognosy of Xigui. J Anhui Agric Sci 35(8):2307–2425. https://doi.org/10.1398/j.cnki.0517-6611.2007.08.059
Zhu B, Feng Q, Yu J, Yu Y, Zhu XX, Wang Y, Guo J, Hu X, Cai MX (2020) Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae). PLoS ONE 15(9):e239823. https://doi.org/10.1371/journal.pone.0239823
Acknowledgements
We thank Dr. Jun Qian of Biozeron Biotech Co. Ltd., Shanghai, China, for his assistance in data analysis and the anonymous reviewers for helpful comments and valuable views on the manuscript.
Funding
This work was supported by the Major Projects of Science and Technology Plan of Dali state (D2019NA03) and Li Jian Expert Workstation of Yunnan Province (202005AF150013).
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Conceptualization, YG and CX; methodology, CX and BD; software, YG and WL; investigation, YG and CX; resources, YG; CX; BD; HZ; XC; YW; writing—original draft preparation, YG; writing—review and editing, CX and BD; supervision, CX; project administration, CX; BD; HZ; XC; YW; All authors have read and agreed to the published version of the manuscript.
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Guan, Yh., Liu, Ww., Duan, Bz. et al. The first complete chloroplast genome of Vicatia thibetica de Boiss.: genome features, comparative analysis, and phylogenetic relationships. Physiol Mol Biol Plants 28, 439–454 (2022). https://doi.org/10.1007/s12298-022-01154-y
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DOI: https://doi.org/10.1007/s12298-022-01154-y