Plant Cell Reports

, Volume 25, Issue 12, pp 1369–1379 | Cite as

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

  • Hwa-Jee Chung
  • Jong Duk Jung
  • Hyun-Woo Park
  • Joo-Hwan Kim
  • Hyun Wook Cha
  • Sung Ran Min
  • Won-Joong Jeong
  • Jang Ryol Liu
Genetics and Genomics

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.

Keywords

Cultivated potato (Solanum tuberosum L. cv. Desiree) Chloroplast genome sequence Indels Intergenic region Open reading frame (ORF) 

Notes

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.

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Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Hwa-Jee Chung
    • 1
  • Jong Duk Jung
    • 2
  • Hyun-Woo Park
    • 2
  • Joo-Hwan Kim
    • 3
  • Hyun Wook Cha
    • 1
  • Sung Ran Min
    • 1
  • Won-Joong Jeong
    • 1
  • Jang Ryol Liu
    • 1
  1. 1.Plant Genomics Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)DaejeonKorea
  2. 2.Laboratory of Functional Genomics for Plant Secondary MetabolismEugentech Inc.DaejeonKorea
  3. 3.Department of Life ScienceDaejeon UniversityDaejeonKorea

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