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Characterization of the complete chloroplast genome of Nitraria tangutorum, a desert shrub

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Abstract

The chloroplast genome sequence of Nitraria tangutorum, a desert shrub, was sequenced using high-throughput sequencing technology and analysed phylogenetically in the present study. The chloroplast genome is 159,414 bp in length, including a large single copy region of 87,924 bp and small single copy region of 18,318 bp, and a pair of inverted repeat regions of 26,586 bp. The chloroplast genome contains 110 unique genes, including 77 protein-coding genes, four ribosomal RNA genes, and 29 tRNA genes. Most of these genes are present as a single copy and in two or more copies 19 genes occurred. Seventeen genes have one intron, and clpP and ycf3 genes contain two introns. A total of 81 simple sequence repeats (SSRs) were identified, most of them were found to be mononucleotide repeats composed of A/T. In addition to SSRs, 66 repeats were identified, including 41 tandem repeats, 10 palindromic repeats, and 15 forward repeats. The phylogenetic analysis based on 54 protein-coding genes demonstrated a close relationship between N. tangutorum and other plant species in Sapindales. The complete chloroplast genome sequence of N. tangutorum will provide important data for further study of taxonomy and systematics of the genus Nitraria.

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References

  • Bankevich A., Nurk S., Antipov D, Gurevich A. A., Dvorkin M., Kulikov A. S. et al. 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477.

    Article  CAS  Google Scholar 

  • Doyle J. J. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15.

    Google Scholar 

  • Katoh K. and Standley D. M. 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780.

    Article  CAS  Google Scholar 

  • Liu Y. and Zhou L. 2003 Nitrariaceae. In Flora of China (ed. Z. Wu and P. Raven), vol. 11, pp. 41–42. Science Press, Beijing.

  • Liu Z., Mei L., Wang Q., Shao Y. and Tao Y. 2014 Optimization of subcritical fluid extraction of seed oil from Nitraria tangutorum using response surface methodology. LWT- Food Sci. Technol. 56, 168–174.

    Article  CAS  Google Scholar 

  • Lohse M., Drechsel O., Kahlau S. and Bock R. 2013 Organellar genome DRAW: a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41, 575–581.

    Article  Google Scholar 

  • Parks M., Cronn R. and Liston A. 2009 Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 7, 84.

    Article  Google Scholar 

  • Stamatakis A. 2014 RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.

    Article  CAS  Google Scholar 

  • Stevens P. F. 2001 Angiosperm phylogeny website, version 14, July 2017. http://www.mobot.org/MOBOT/research/APweb/ (accessed 30 June 2019).

  • Wyman S. K., Jansen R. K. and Boore J. L. 2004 Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20, 3252–3255.

    Article  CAS  Google Scholar 

  • Xu L. and Huang C. (ed.) 1998 Zygophyllaceae. In Flora reipublicae popularis sinicae, vol. 43, pp. 122–123. Science Press, Beijing.

  • Yan Y. Q., Pan C. H., Du Y. L., Li D. Y. and Liu W. 2018 Exogenous salicylic acid regulates reactive oxygen species metabolism and ascorbate–glutathione cycle in Nitraria tangutorum Bobr. under salinity stress. Physiol. Mol. Biol. Plants. 24, 577–589.

    Article  CAS  Google Scholar 

  • Yang Y. L., Yang F., Li X. N., Shi R. X. and Lu J. 2013 Signal regulation of proline metabolism in callus of the halophyte Nitraria tangutorum Bobr. grown under salinity stress. Plant Cell Tiss. Org. Cult. 112, 33–42.

    Article  Google Scholar 

  • Yang Y., Shi R., Wei X., Fan Q. and An L. 2010 Effect of salinity on antioxidant enzymes in calli of the halophyte Nitraria tangutorum Bobr. Plant Cell Tiss. Org. Cult. 102, 387–395.

    Article  CAS  Google Scholar 

  • Zhao J. Q., Wang Y. M., Yang Y. L., Zeng Y., Wang Q. L., Shao Y. et al. 2017 Isolation and identification of antioxidant and \(\upalpha \)-glucosidase inhibitory compounds from fruit juice of Nitraria tangutorum. Food Chem. 227, 93–101.

  • Zheng L. L., Dang Z. H., Li H. Y., Zhang H. R., Wu S. B. and Wang Y. C. 2014 Isolation and characterization of a \(\Delta \)1-pyrroline-5-carboxylate synthetase (NtP5CS) from Nitraria tangutorum Bobr. and functional comparison with its Arabidopsis homologue. Mol. Biol. Rep. 41, 563–572.

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31670335, 31570407, and 31770363) and the Ministry of Education of China through 111 and ‘Double First-Class’projects, grant number B08044 and Yldxxk201819.

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Authors and Affiliations

  1. College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, People’s Republic of China

    Merhaba Abla, Xi Zha, Ying Wang, Xiao Yang Wang, Fei Gao, Yijun Zhou & Jinchao Feng

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  1. Merhaba Abla
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  2. Xi Zha
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  3. Ying Wang
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  4. Xiao Yang Wang
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  5. Fei Gao
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  6. Yijun Zhou
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  7. Jinchao Feng
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Correspondence to Fei Gao.

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Corresponding editor: Manoj Prasad

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Abla, M., Zha, X., Wang, Y. et al. Characterization of the complete chloroplast genome of Nitraria tangutorum, a desert shrub. J Genet 98, 91 (2019). https://doi.org/10.1007/s12041-019-1135-9

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  • DOI: https://doi.org/10.1007/s12041-019-1135-9

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