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BY-NC-ND 3.0 license Open Access Published by De Gruyter July 3, 2007

The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis

  • Wojciech Pląder EMAIL logo , Yasushi Yukawa , Masahiro Sugiura and Stefan Malepszy

Abstract

The complete nucleotide sequence of the cucumber (C. sativus L. var. Borszczagowski) chloroplast genome has been determined. The genome is composed of 155,293 bp containing a pair of inverted repeats of 25,191 bp, which are separated by two single-copy regions, a small 18,222-bp one and a large 86,688-bp one. The chloroplast genome of cucumber contains 130 known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat region. Of these genes, 16 contain one intron, and two genes and one ycf contain 2 introns. Twenty-one small inversions that form stem-loop structures, ranging from 18 to 49 bp, have been identified. Eight of them show similarity to those of other species, while eight seem to be cucumber specific. Detailed comparisons of ycf2 and ycf15, and the overall structure to other chloroplast genomes were performed.

[1] Havey, M.J., Lilly, J.W., Bohanec, B., Bartoszewski, G. and Malepszy, S. Cucumber: A model angiosperm for mitochondrial transformation? J. Appl. Genet. 43 (2002) 1–17. Search in Google Scholar

[2] Kolodner, R. and Tewari, K. Molecular size and conformation of chloroplast deoxyrybonucleic acid from pea leaves. J. Biol. Chem. 247 (1972) 6355–6364. Search in Google Scholar

[3] Kolodner, R. and Tewari, K. Inverted repeats in chloroplast DNA from higher plants. Proc. Natl. Acad. Sci. USA 76 (1979) 41–45. http://dx.doi.org/10.1073/pnas.76.1.4110.1073/pnas.76.1.41Search in Google Scholar

[4] Deng, X.W., Wing, R.A. and Gruissem, A. The chloroplast genome exists in multimeric forms. Proc. Natl. Acad. Sci. USA 86 (1989) 4156–4160. http://dx.doi.org/10.1073/pnas.86.11.415610.1073/pnas.86.11.4156Search in Google Scholar

[5] Lilly, J.W., Havey, M.J., Jackson, S.A. and Jiang, J. Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell 13 (2001) 245–254. http://dx.doi.org/10.1105/tpc.13.2.24510.1105/tpc.13.2.245Search in Google Scholar

[6] Hoshi, Y., Plader, W. and Malepszy, S. New C-banding pattern for chromosome identification in cucumber (Cucumis sativus L.). Plant Breed. 117 (1998) 77–82. http://dx.doi.org/10.1111/j.1439-0523.1998.tb01452.x10.1111/j.1439-0523.1998.tb01452.xSearch in Google Scholar

[7] De Nisi, P. and Zocchi, G. Phosphoenolpyruvate carboxylase in cucumber (Cucumis sativus L.) roots under iron deficiency: activity and kinetic characterization. J. Exp. Biol. 51 (2000) 1903–1909. Search in Google Scholar

[8] Hirano, T., Kiyota, M. and Aiga I. Physical effects of dust on leaf physiology of cucumber and kidney bean plants. Environ. Pollut. 89 (1995) 255–261. http://dx.doi.org/10.1016/0269-7491(94)00075-O10.1016/0269-7491(94)00075-OSearch in Google Scholar

[9] Burza, W. and Malepszy, S. Direct plant regeneration from leaf explants in cucumber (C. sativus sativus L.) is free of stable genetic variation. Plant Breed. 114 (1995a) 341–345. http://dx.doi.org/10.1111/j.1439-0523.1995.tb01246.x10.1111/j.1439-0523.1995.tb01246.xSearch in Google Scholar

[10] Wróblewski, T., Filipecki, M.K. and Malepszy, S. Factors influencing cucumber (C. sativus sativus L.) somatic embryogenesis. I. The crucial role of pH and nitrogen in suspension culture. Acta Soc. Bot. Pol. 64 (1995) 223–231. Search in Google Scholar

[11] Burza, W. and Malepszy, S. In vitro culture of C.sativus sativus L. XVIII. Plants from protoplasts through direct somatic embryogenesis. Plant Cell Tissue Organ Cult. 41 (1995b) 259–266. http://dx.doi.org/10.1007/BF0004509010.1007/BF00045090Search in Google Scholar

[12] Yin, Z. and Malepszy, S. The transgenes are expressed with different level in plants. Biotechnologia 2 (2003) 236–260. Search in Google Scholar

[13] Yin, Z., Plader, W. and Malepszy, S. Transgene inheritance in plants. J. Appl. Genet. 45 (2004) 127–144. Search in Google Scholar

[14] Havey, M.J., Lilly, J.W., Bohanec, B., Bartoszewski, G. and Malepszy, S. Cucumber: a model angiosperm for mitochondrial transformation? J. Appl. Genet. 43 (2002) 1–17. Search in Google Scholar

[15] Palmer, J.D. Physical and gene mapping of chloroplast DNA from Atriplex triangularis and C. sativus sativa. Nucleic Acid Res. 10 (1982) 1593–1605. http://dx.doi.org/10.1093/nar/10.5.159310.1093/nar/10.5.1593Search in Google Scholar PubMed PubMed Central

[16] Kim, J.S., Jung, J.D., Lee, J.A., Park, H.W., Oh, K.H., Jeong, W.J., Choi, D.W., Liu, J.R. and Cho, K.Y. Complete sequence and organization of the cucumber (C. sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell. Rep. 25 (2006) 334–340. http://dx.doi.org/10.1007/s00299-005-0097-y10.1007/s00299-005-0097-ySearch in Google Scholar PubMed

[17] Cheng, M.C., Wu, S.P., Chen, L.F. and Chen, S.C. Identification and purification of a spinach chloroplast DNA-binding protein that interacts specifically with the plastid psaA-psaB-rps14 promoter region. Planta 203 (1997) 373–380. http://dx.doi.org/10.1007/s00425005020310.1007/s004250050203Search in Google Scholar PubMed

[18] Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chungwonse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohto, C., Torazawa, K., Meng, B.Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kato, A., Tohdoh, N., Shimada, H. and Sugiura, M. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5 (1986) 2043–2049. Search in Google Scholar

[19] Higgins, D., Thompson, J., Gibson, T., Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673–4680. http://dx.doi.org/10.1093/nar/22.22.467310.1093/nar/22.22.4673Search in Google Scholar PubMed PubMed Central

[20] Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R. and Miller, W. PipMaker-a web server for aligning two genomic DNA sequences. Genome Res. 10 (2000) 577–586. http://dx.doi.org/10.1101/gr.10.4.57710.1101/gr.10.4.577Search in Google Scholar PubMed PubMed Central

[21] Maier, R.M., Neckermann, K., Igloi, G.L. and Kossel, H. Complete sequence of the maize chloroplast genome: gene content. hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251 (1995) 614–628. http://dx.doi.org/10.1006/jmbi.1995.046010.1006/jmbi.1995.0460Search in Google Scholar PubMed

[22] Kim, K.J. and Lee, H.L. Complete chloroplast genome sequence from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11 (2004) 247–261. http://dx.doi.org/10.1093/dnares/11.4.24710.1093/dnares/11.4.247Search in Google Scholar PubMed

[23] Kim, K.J. and Lee, H.L. Widespread occurance of small inversions in the chloroplast genomes of land plants. Mol. Cells 19 (2005) 104–113. Search in Google Scholar

[24] Palmer, J.D. Plastid chromosomes: structure and evolution In: Cell Culture and Somatic Cell Genetics in Plants, Vol. 7A, The Molecular Biology of Plastids (Vasil, I.K. and Bogorad, L. Eds.), Academic Press, San Diego, 1991, 5–53. Search in Google Scholar

[25] Kelchner, S.A. and Wende, J.F. Hairpins create minute inversions in noncoding regions of chloroplast DNA. Curr. Genet. 30 (1996) 259–262. http://dx.doi.org/10.1007/s00294005013010.1007/s002940050130Search in Google Scholar PubMed

[26] Shinozaki, K., Hayashida, N. and Sugiura, M. Nicotiana chloroplast genes for components of the photosynthetic apparatus. Photosynthesis Res. 18 (1988) 7–31. http://dx.doi.org/10.1007/BF0004297810.1007/BF00042978Search in Google Scholar PubMed

Published Online: 2007-7-3
Published in Print: 2007-12-1

© 2007 University of Wrocław, Poland

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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