Skip to main content
SpringerLink
Log in

The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence

  • Genetics and Genomics
  • Published:
Plant Cell Reports Aims and scope Submit manuscript

Abstract

The complete nucleotide sequence of the chloroplast genome of potato Solanum tuberosum L. cv. Desiree was determined. The circular double-stranded DNA, which consists of 155,312 bp, contains a pair of inverted repeat regions (IRa, IRb) of 25,595 bp each. The inverted repeat regions are separated by small and large single copy regions of 18,373 and 85,749 bp, respectively. The genome contains 79 proteins, 30 tRNAs, 4 rRNAs, and unidentified genes. A comparison of chloroplast genomes of seven Solanaceae species revealed that the gene content and their relative positions of S. tuberosum are similar to the other six Solanaceae species. However, undefined open reading frames (ORFs) in LSC region were highly diverged in Solanaceae species except N. sylvestris. Detailed comparison was identified by numerous indels in the intergenic regions that were mostly located in the LSC region. Among them, a single large 241-bp deletion, was not associated with direct repeats and found in only S. tuberosum, clearly discriminates a cultivated potato from wild potato species Solanum bulbocastanum. The extent of sequence divergence may provide the basis for evaluating genetic diversity within the Solanaceae species, and will be useful to examine the evolutionary processes in potato landraces.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Asano T, Tsudzuki T, Takahashi S, Shimada H, Kadowaki K (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res 11:93–99

    Article  PubMed  CAS  Google Scholar 

  • Boudreau E, Turmel M, Goldschmidt-Clermont M, Rochaix JD, Sivan S, Michaels A, Leu S (1997) A large open reading frame (orf1995) in the chloroplast DNA of Chlamydomonas reinhardtii encodes an essential protein. Mol Gen Genet 253:649–653

    Article  PubMed  CAS  Google Scholar 

  • Calsa Junior T, Carraro DM, Benatti MR, Barbosa AC, Kitajima JP, Carrer H (2004) Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet 46:366–373

    Article  PubMed  CAS  Google Scholar 

  • Cosner ME, Raubeson LA, Jansen RK (2004) Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol Biol 4:1471–2148

    Article  Google Scholar 

  • Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen RK (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 1432–2242 (on line)

  • Drescher A, Ruf S, Calsa T Jr., Carrer H, Bock R (2000) The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J 22:97–104

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202

    PubMed  CAS  Google Scholar 

  • Guo CH, Terachi T (2005) Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis. Genes Genet Syst 80:277–285

    Article  PubMed  CAS  Google Scholar 

  • Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L (2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods Enzymol 395:348–384

    Article  PubMed  CAS  Google Scholar 

  • Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S (2000) Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res 7:323–330

    Article  PubMed  CAS  Google Scholar 

  • Kawagoe Y, Kikuta Y (1991) Chloroplat DNA evolution in potato (Solanum tuberosum L.). Theor Appl Genet 81:13–20

    Article  CAS  Google Scholar 

  • Kim KJ, Choi KS, Jansen RK (2005) Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol Biol Evol 22:1783–1792

    Article  PubMed  CAS  Google Scholar 

  • 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 11:247–261

    Article  PubMed  CAS  Google Scholar 

  • Kim KJ, Lee HL (2005) Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells 19:104–113

    PubMed  CAS  Google Scholar 

  • Kode V, Mudd EA, Iamtham S, Day A (2005) The tobacco plastid accD gene is essential and is required for leaf development. Plant J 44:237–244

    Article  PubMed  CAS  Google Scholar 

  • Madoka Y, Tomizawa K, Mizoi J, Nishida I, Nagano Y, Sasaki Y (2002) Chloroplast transformation with modified accD operon increases acetyl-CoA carboxylase and causes extension of leaf longevity and increase in seed yield in tobacco. Plant Cell Physiol 43:1518–1525

    Article  PubMed  CAS  Google Scholar 

  • Maier RM, Neckermann K, Igloi GL, Kossel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614–628

    Article  PubMed  CAS  Google Scholar 

  • Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N et al. (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics 266:740–746

    Article  PubMed  CAS  Google Scholar 

  • Ogihara Y, Terachi T, Sasakuma T (1991) Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region. Genetics 129:873–884

    PubMed  CAS  Google Scholar 

  • Oharamays EP, Capwell JC (1993) Miniprep for chloroplast DNA isolation. Microchem J 47:245–250

    Article  CAS  Google Scholar 

  • Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK (2005) Complete chloroplast genome sequence of glycine max and comparative analyses with other legume genomes. Plant Mol Biol 59:309–322

    Article  PubMed  CAS  Google Scholar 

  • Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19:1602–1612

    PubMed  CAS  Google Scholar 

  • Shahid Masood M, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T, Kadowaki K (2004) The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 340:133–139

    Article  PubMed  CAS  Google Scholar 

  • Shinozaki K, Ohme M, Tanaka K, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Cuhunwongse J, Obokata J, Yamaguchi-Shinozaki K et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO J 5:2043–2049

    PubMed  CAS  Google Scholar 

  • Spooner DM, Nunez J, Rodriguez F, Naik PS, Ghislain M (2005) Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato. Theor Appl Genet 110:1020–1026

    Article  PubMed  CAS  Google Scholar 

  • Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (2003) Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res 31:5324–5331

    Article  PubMed  CAS  Google Scholar 

  • Sugiura M, Hirose T, Sugita M (1998) Evolution and mechanism of translation in chloroplasts. Annu Rev Genet 32:437–459

    Article  PubMed  CAS  Google Scholar 

  • Swofford DL (1998) PAUP*—Phylogenetic analysis using parsimony, ver. 4.0 beta 10. Sunderland: Sinauer Associates

    Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acid Res 24:4876–4882

    Article  Google Scholar 

  • Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255

    Article  PubMed  CAS  Google Scholar 

  • Yukawa M, Tsudzuki T, Sugiura M (2006) The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics:1–7

Download references

Acknowledgements

This work was supported by a grant to JRL from the Crop Functional Genomics Center of the 21st Century Frontier Research Program, a grant to JRL from the Korea Science and Engineering Foundation through the Plant Metabolism Research Center of the Kyung Hee University funded by the Korea Ministry of Science and Technology, and a grant to JRL from the Marine and Extreme Genome Research Center Program funded by the Korean Ministry of Marine Affairs and Fisheries.

Author information

Authors and Affiliations

  1. Plant Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 305-333, Korea

    Hwa-Jee Chung, Hyun Wook Cha, Sung Ran Min, Won-Joong Jeong & Jang Ryol Liu

  2. Laboratory of Functional Genomics for Plant Secondary Metabolism, Eugentech Inc., Daejeon, 305-333, Korea

    Jong Duk Jung & Hyun-Woo Park

  3. Department of Life Science, Daejeon University, Daejeon, 300-716, Korea

    Joo-Hwan Kim

Authors
  1. Hwa-Jee Chung
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jong Duk Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hyun-Woo Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Joo-Hwan Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hyun Wook Cha
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sung Ran Min
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Won-Joong Jeong
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jang Ryol Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jang Ryol Liu.

Additional information

Communicated by I. S. Chung

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chung, HJ., Jung, J.D., Park, HW. et al. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep 25, 1369–1379 (2006). https://doi.org/10.1007/s00299-006-0196-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00299-006-0196-4

Keywords

Search

Navigation