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Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis

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Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semi-desert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides.

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  1. Benson G. 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580.

  2. Cardoso D., Pennington R. T., De Queiroz L. P., Boatwright J. S., Van Wyk B. E., Wojciechowski M. F. et al. 2013 Reconstructing the deep-branching relationships of the papilionoid legumes. S. Afr. J. Bot. 89, 58–75.

  3. Civáň P., Foster P. G., Embley M. T, Seneca A. and Cox C. J. 2014 Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants. Genome Biol. Evol. 6, 897–911.

  4. Daniell H., Lin C. S., Yu M. and Chang W. J. 2016 Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 17, 134.

  5. Darling A. C., Mau B., Blattner F. R. and Perna N. T. 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403.

  6. Derrien T., André C., Galibert F. and Hitte C. 2006 AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps. Bioinformatics 23, 498–499.

  7. Downie S. R., Llanas E. and Katz-Downie D. S. 1996 Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNAs. Syst. Bot. 21, 135–151.

  8. Doyle J. J., Doyle J. L., Ballenger J. A. and Palmer J. D. 1996 The distribution and phylogenetic significance of a 50-kb chloroplast DNA inversion in the flowering plant family Leguminosae. Mol. Phylogenet. Evol. 5, 429–438.

  9. Gantt J. S., Baldauf S. L., Calie P. J., Weeden N. F. and Palmer J. D. 1991 Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 10, 3073–3078.

  10. Iinuma M., Ohyama M. and Tanaka T. 1995 Six flavonostilbenes and a flavanone in roots of Sophora alopecuroides. Phytochemistry 38, 519–525.

  11. Jansen R. K. and Palmer J. D. 1987 Chloroplast DNA from lettuce and Barnadesia (Asteraceae): structure, gene localization, and characterization of a large inversion. Curr. Genet. 11, 553–564.

  12. Jansen R. K., Saski C., Lee S. B, Hansen A. K. and Daniell H. 2010 Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol. Biol. Evol. 28, 835–847.

  13. Kumar S., Stecher G., Li M., Knyaz C. and Tamura K. 2018 MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549.

  14. Kurtz S., Choudhuri J. V., Ohlebusch E., Schleiermacher C., Stoye J. and Giegerich R. 2001 REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29, 4633–4642.

  15. Lagesen K., Hallin P., Rødland E. A., Stærfeldt H. H., Rognes T. and Ussery D. W. 2007 RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108.

  16. Lemieux C., Otis C. and Turmel M. 2016 Comparative chloroplast genome analyses of streptophyte green algae uncover major structural alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae. Front. Plant Sci. 7, 697.

  17. Li J. G., Yang X. Y. and Huang W. 2016 Total alkaloids of Sophora alopecuroides inhibit growth and induce apoptosis in human cervical tumor hela cells in vitro. Pharmacogn. Mag. 12, S253.

  18. Liang L., Wang X. Y., Zhang X. H., Ji B., Yan H. C., Deng H. Z. et al. 2012 Sophoridine exerts an anti-colorectal carcinoma effect through apoptosis induction in vitro and in vivo. Life Sci. 91, 1295–1303.

  19. Lohse M., Drechsel O. and 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, 267–274.

  20. Lowe T. M. and Eddy S. R. 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964.

  21. Lu X., Lin B., Tang J. G., Cao Z. and Hu Y. 2014 Study on the inhibitory effect of total alkaloids of Sophora alopecuroides on osteosarcoma cell growth. Afr. J. Tradit. Complement. Altern. Med. 11, 172–175.

  22. Luo R., Liu B., Xie Y., Li Z., Huang W., Yuan J. 2012 SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18.

  23. Martin G. E., Rousseau-Gueutin M., Cordonnier S., Lima O., Michon-Coudouel S, Naquin D. et al. 2014 The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Ann. Bot. 113, 1197–1210.

  24. Palmer J. D., Osorio B. and Thompson W. F. 1988 Evolutionary significance of inversions in legume chloroplast DNAs. Curr. Genet. 14, 65–74.

  25. Park I., Yang S., Choi G., Kim W. J. and Moon B. C. 2017 The complete chloroplast genome sequences of aconitum pseudolaeve and aconitum longecassidatum, and development of molecular markers for distinguishing species in the aconitum subgenus lycoctonum. Molecules 22, 2012.

  26. 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.

  27. Powell W., Morgante M., McDevitt R., Vendramin G. G. and Rafalski J. A. 1995 Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. USA 92, 7759–7763.

  28. Tanaka T., Ohyama M., Iinuma M., Shirataki Y. and Komatsu M. 1998 Isoflavonoids from Sophora secundiflora, S. arizonica and S. gypsophila. Phytochemistry 48, 1187–1193.

  29. Tangphatsornruang S., Sangsrakru D., Chanprasert J., Uthaipaisanwong P., Yoocha T, Jomchai N. et al. 2009 The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res. 17, 11–22.

  30. Tillich M., Lehwark P., Pellizzer T., Ulbricht-Jones E. S., Fischer A., Bock R. et al. 2017 GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45, W6–W11.

  31. Tonti‐Filippini J., Nevill P. G., Dixon K. and Small I. 2017 What can we do with 1000 plastid genomes? Plant J. 90, 808–818.

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

  33. Wicke S., Schneeweiss G. M., Müller K. F., dePamphilis C. W. and Quandt D. 2011 The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol. Biol. 76, 273–297.

  34. Wunderlin R. 1982 The Leguminosae: a source book of characteristics, uses, and nodulation. Econ. Bot. 36, 224–224.

  35. Yang Y., Zhou T., Duan D., Yang J., Feng L. and Zhao G. 2016 Comparative analysis of the complete chloroplast genomes of five Quercus species. Front. Plant Sci. 7, 959.

  36. Yang Z., Huang Y., An W., Zheng X., Huang S. and Liang L. 2019 Sequencing and structural analysis of the complete chloroplast genome of the medicinal plant Lycium chinense mill. Plants 8, 87.

  37. Zhang L., Zheng Y., Deng H., Liang L. and Peng J. 2014a Aloperine induces G2/M phase cell cycle arrest and apoptosis in HCT116 human colon cancer cells. Int. J. Mol. Med. 33, 1613–1620.

  38. Zhang Y., Ma J., Yang B., Li R., Zhu W., Sun L. et al. 2014b The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species. Gene 540, 201–209.

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This research was funded by the National Natural Science Foundation of China, grant numbers 31770363 and 31670335, and the Ministry of Education of China through 111 and Double First-Class Projects, grant numbers B08044 and Yldxxk201819.

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Correspondence to Fei Gao or Yijun Zhou.

Additional information

Corresponding editor: H. A. Ranganath

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Zha, X., Wang, X., Li, J. et al. Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet 99, 13 (2020). https://doi.org/10.1007/s12041-019-1173-3

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  • chloroplast genome
  • comparative genomics
  • phylogenetic analysis
  • IR region
  • Sophora alopecuroides.