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Complete chloroplast genome of Campsis grandiflora (Thunb.) schum and systematic and comparative analysis within the family Bignoniaceae

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Abstract

Background

Plants belonging to the Bignoniaceae family have a wide distribution in the tropics and large populations around the world. However, limited information is available about Bignoniaceae. This study aimed to obtain more research information about Bignoniaceae plants and provide data support for the study of plant plastid genomes.

Methods and results

In the present study, we focused on the chloroplast genome bio-information of Campsis grandiflora. The chloroplast DNA of C. grandiflora was extracted, sequenced, assembled, and annotated with corresponding software. Results show that the complete chloroplast genome of C. grandiflora is 154,303 bp in length and has a quadripartite structure with large single copy of 85,064 bp and a small single copy of 18,009 bp separated by inverted repeats of 25,615 bp. A total of 110 genes in C. grandiflora comprised 79 protein-coding genes, 27 transfer RNA genes, and 4 ribosomal RNA genes. The distribution of simple sequence repeats and long repeat sequences was determined. We carried out phylogenetic analysis based on homologous amino acid sequence among 45 species derived from Bignoniaceae. Compared with the chloroplast genome of A. thaliana, an inversion was identified in that of C. grandiflora, which result in the incomplete clpP gene.

Conclusions

The chloroplast genomes were used for molecular marker, species identification, and phylogenetic studies. The outcome strongly supported that C. grandiflora and genus Incarvillea formed a cluster within Bignoniaceae. This study identified the unique characteristics of the C. grandiflora cp. genome, thus providing theoretical basis for species identification and biological research.

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Data availability

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW430049. The associated BioProject, BioSample and SRA numbers are PRJNA704532, SAMN18043523, and SRR13776395, respectively.

References

  1. Liu C, Huang L-F (2020) Chloroplast genomic maps of Chinese medicinal plants [M], vol 1. Science Press, Beijing, China, pp 3–4

  2. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364. https://doi.org/10.1155/2012/251364

    Article  PubMed  PubMed Central  Google Scholar 

  3. Lohmann LG (2006) Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae). Am J Bot 93(2):304–318. https://doi.org/10.3732/ajb.93.2.304

    Article  CAS  PubMed  Google Scholar 

  4. Flora of China (2021) Bignoniaceae. IBCAS Publishing iPlant. http://www.iplant.cn/info/Bignoniaceae?t=z. Accessed 07 Jan 2021

  5. Flora of China (2021) Campsis grandiflora. IBCAS Publishing iPlant. http://www.iplant.cn/info/Campsis%20grandiflora?t=foc. Accessed 07 Jan 2021

  6. Cui XY, Kim JH, Zhao X, Chen BQ, Lee BC, Pyo HB, Yun YP, Zhang YH (2006) Antioxidative and acute anti-inflammatory effects of Campsis grandiflora flower. J Ethnopharmacol 103(2):223–228. https://doi.org/10.1016/j.jep.2005.08.007

    Article  PubMed  Google Scholar 

  7. Commission CP (2015) The Pharmacopoeia of the People’s Republic of China, 2015 edition part I. China Medical Science Press, Beijing

    Google Scholar 

  8. Xiao P-g, Zhao Z-z (2018) Encyclopedia of medicinal plants. World Book Inc, Beijing, China, pp 11–14

    Google Scholar 

  9. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, McVeigh R, O’Neill K, Robbertse B, Sharma S, Soussov V, Sullivan JP, Sun L, Turner S, Karsch-Mizrachi I (2020) NCBI taxonomy: a comprehensive update on curation, resources and tools. Database. https://doi.org/10.1093/database/baaa062

    Article  PubMed  PubMed Central  Google Scholar 

  10. Steemers FJ, Gunderson KL (2005) Illumina, Inc. Pharmacogenomics 6:777–782. https://doi.org/10.2217/14622416.6.7.777

    Article  PubMed  Google Scholar 

  11. Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45(4):e18. https://doi.org/10.1093/nar/gkw955

    Article  CAS  PubMed  Google Scholar 

  12. Shi L, Chen H, Jiang M, Wang L, Wu X, Huang L, Liu C (2019) CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res 47(W1):W65–W73. https://doi.org/10.1093/nar/gkz345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hasegawa M, Kishino H, Saitou N (1991) On the maximum likelihood method in molecular phylogenetics. J Mol Evol 32(5):443–445. https://doi.org/10.1007/BF02101285

    Article  CAS  PubMed  Google Scholar 

  14. Nguyen L-T, 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

    Article  CAS  PubMed  Google Scholar 

  15. Fonseca LHM, Lohmann LG (2017) Plastome rearrangements in the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae) and Its phylogenetic implications. Front Plant Sci 8:1875. https://doi.org/10.3389/fpls.2017.01875

    Article  PubMed  PubMed Central  Google Scholar 

  16. Fonseca LHM, Lohmann LG (2018) Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae). Mol Phylogenet Evol 123:1–15. https://doi.org/10.1016/j.ympev.2018.01.023

    Article  CAS  PubMed  Google Scholar 

  17. Thode VA, Lohmann LG (2019) Comparative chloroplast genomics at low taxonomic levels: a case study using Amphilophium (Bignonieae, Bignoniaceae). Front Plant Sci 10:796. https://doi.org/10.3389/fpls.2019.00796

    Article  PubMed  PubMed Central  Google Scholar 

  18. Firetti F, Zuntini AR, Gaiarsa JW, Oliveira RS, Lohmann LG, Van Sluys MA (2017) Complete chloroplast genome sequences contribute to plant species delimitation: a case study of the Anemopaegma species complex. Am J Bot 104(10):1493–1509. https://doi.org/10.3732/ajb.1700302

    Article  CAS  PubMed  Google Scholar 

  19. Nazareno AG, Carlsen M, Lohmann LG (2015) Complete chloroplast genome of Tanaecium tetragonolobum: the first Bignoniaceae plastome. PLoS ONE 10(6):e0129930. https://doi.org/10.1371/journal.pone.0129930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Fonseca LH, Cabral SM, Agra Mde F, Lohmann LG (2015) Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae). PhytoKeys 46:35–43. https://doi.org/10.3897/phytokeys.46.8421

    Article  Google Scholar 

  21. Jiang Y, Wang J, Qian J, Xu L, Duan B (2020) The complete chloroplast genome sequence of Oroxylum indicum (L.) Kurz (Bignoniaceae) and its phylogenetic analysis. Mitochondrial DNA B 5(2):1429–1430. https://doi.org/10.1080/23802359.2020.1736961

    Article  Google Scholar 

  22. Ma Q-g, Zhang J-g, Zhang J-p (2020) The complete chloroplast genome of Catalpa ovata G. Don.(Bignoniaceae). Mitochondrial DNA B 5(2):1800–1801. https://doi.org/10.1080/23802359.2020.1750979

    Article  Google Scholar 

  23. Yang J, Wang S, Huang Z, Guo P (2020) The complete chloroplast genome sequence of Catalpa bungei (Bignoniaceae): a high-quality timber species from China. Mitochondrial DNA B 5(4):3854–3855. https://doi.org/10.1080/23802359.2020.1841581

    Article  Google Scholar 

  24. Wu X, Li H, Chen S (2021) Characterization of the chloroplast genome and its inference on the phylogenetic position of Incarvillea sinensis Lam.(Bignoniaceae). Mitochondrial DNA B 6(1):263–264. https://doi.org/10.1080/23802359.2020.1860722

    Article  Google Scholar 

  25. Ma G-T, Yang J-G, Zhang Y-F, Guan T-X (2019) Characterization of the complete chloroplast genome of Incarvillea arguta (Bignoniaceae). Mitochondrial DNA B 4(1):1603–1604. https://doi.org/10.1080/23802359.2019.1601529

    Article  Google Scholar 

  26. Wu X, Peng C, Li Z, Chen S (2019) The complete plastome genome of Incarvillea compacta (Bignoniaceae), an alpine herb endemic to China. Mitochondrial DNA B 4(2):3786–3787. https://doi.org/10.1080/23802359.2019.1681916

    Article  Google Scholar 

  27. Wang Y, Yuan X, Li Y, Zhang J (2019) The complete chloroplast genome sequence of Spathodea campanulata. Mitochondrial DNA B 4(2):3469–3470. https://doi.org/10.1080/23802359.2019.1674710

    Article  Google Scholar 

  28. Yi D-K, Kim K-J (2016) Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa. Mitochondrial DNA B 1(1):627–629. https://doi.org/10.1080/23802359.2016.1214546

    Article  Google Scholar 

  29. Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6(5):283–290. https://doi.org/10.1093/dnares/6.5.283

    Article  CAS  PubMed  Google Scholar 

  30. Zhang D, Gao F, Jakovlic I, Zou H, Zhang J, Li WX, Wang GT (2020) PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 20(1):348–355. https://doi.org/10.1111/1755-0998.13096

    Article  PubMed  Google Scholar 

  31. Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23(1):127–128. https://doi.org/10.1093/nar/gkab301

    Article  CAS  PubMed  Google Scholar 

  32. Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583–2585. https://doi.org/10.1093/bioinformatics/btx198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Gojman B, DeHon AVMATCH (2009) : Using logical variation to counteract physical variation in bottom-up, nanoscale systems. In: 2009 International Conference on Field-Programmable Technology, IEEE, pp 78-87. https://doi.org/10.1109/FPT.2009.5377684

  35. Krumsiek J, Arnold R, Rattei T (2007) Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23(8):1026–1028. https://doi.org/10.1093/bioinformatics/btm039

    Article  CAS  PubMed  Google Scholar 

  36. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27(7):1009–1010. https://doi.org/10.1093/bioinformatics/btr039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34(17):3030–3031. https://doi.org/10.1093/bioinformatics/bty220

    Article  CAS  PubMed  Google Scholar 

  38. Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL (2015) Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 32(5):1342–1353. https://doi.org/10.1093/molbev/msv022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhang Z, Li J, Zhao X-Q, Wang J, Wong GK-S, Yu J (2006) KaKs_calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinform 4(4):259–263. https://doi.org/10.1016/S1672-0229(07)60007-2

    Article  CAS  Google Scholar 

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Acknowledgements

We would like to thank Prof. You Jinwen for identifying the plant materials.

Funding

This work was supported by the Chinese Academy of Medical Sciences, Innovation Funds for Medical Sciences (CIFMS) [2021-I2M-1-071 and 2021-I2M-1-022], National Science & Technology Fundamental Resources Investigation Program of China [2018FY100705], National Science Foundation Funds [81872966], and Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau [2020-ZJ-Y20]. The funders were not involved in the study design, data collection, analysis, decision to publish, or manuscript preparation.

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Author notes

  1. Haimei Chen and Zhuoer Chen have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, 100193, Beijing, People’s Republic of China

    Haimei Chen, Mei Jiang & Chang Liu

  2. School of Pharmacy, Xiangnan University, 423000, Chenzhou, Hunan, China

    Zhuoer Chen & Bin Wang

  3. College of Pharmacy, Qinghai Minzu University, 810007, Xining, Qinghai, China

    Qing Du

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  1. Haimei Chen
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Contributions

CL and HMC conceived the study. MJ collected the samples of C. grandiflora, extracted DNA for next-generation sequencing, and assembled and validated the genome. ZEC performed data analysis and drafted the manuscript. HMC, QD and BW reviewed the manuscript critically for important intellectual content. All authors have read and agreed on the contents of the manuscript.

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Correspondence to Chang Liu.

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Chen, H., Chen, Z., Du, Q. et al. Complete chloroplast genome of Campsis grandiflora (Thunb.) schum and systematic and comparative analysis within the family Bignoniaceae. Mol Biol Rep 49, 3085–3098 (2022). https://doi.org/10.1007/s11033-022-07139-0

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