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
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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.
KeywordsCultivated potato (Solanum tuberosum L. cv. Desiree) Chloroplast genome sequence Indels Intergenic region Open reading frame (ORF)
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.
- 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)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 395:348–384PubMedCrossRefGoogle 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 19:1602–1612PubMedGoogle Scholar
- Swofford DL (1998) PAUP*—Phylogenetic analysis using parsimony, ver. 4.0 beta 10. Sunderland: Sinauer AssociatesGoogle 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:1–7Google Scholar