title: 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.
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.
authors.affiliation: Plant Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Korea.
authors.forename: Hwa-Jee
authors.initials: HJ
authors.lastname: Chung
authors.forename: Jong Duk
authors.initials: JD
authors.lastname: Jung
authors.forename: Hyun-Woo
authors.initials: HW
authors.lastname: Park
authors.forename: Joo-Hwan
authors.initials: JH
authors.lastname: Kim
authors.forename: Hyun Wook
authors.initials: HW
authors.lastname: Cha
authors.forename: Sung Ran
authors.initials: SR
authors.lastname: Min
authors.forename: Won-Joong
authors.initials: WJ
authors.lastname: Jeong
authors.forename: Jang Ryol
authors.initials: JR
authors.lastname: Liu
mesh_terms: D000383:Agriculture; D020029:Base Pairing; D001483:Base Sequence; D018742:DNA, Chloroplast / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment; D017384:Sequence Deletion; D012689:Sequence Homology, Nucleic Acid; D011198:Solanum tuberosum / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast; D021901:DNA, Intergenic