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

• Published in: Plant cell reports Vol. 25; no. 12; pp. 1369 - 1379
• Main Authors: CHUNG, Hwa-Jee, JONG DUK JUNG, PARK, Hyun-Woo, KIM, Joo-Hwan, HYUN WOOK CHA, SUNG RAN MIN, JEONG, Won-Joong, JANG RYOL LIU
• Format: Journal Article
• Language: English
• Published: Berlin Springer 01.12.2006; Springer Nature B.V
• Subjects: Agriculture; Bacteria; Base Pairing; Base Sequence; Biological and medical sciences; Biotechnology; Chloroplasts; DNA, Chloroplast - genetics; DNA, Intergenic - genetics; Fundamental and applied biological sciences. Psychology; Genes, Plant; Genes. Genome; Genome, Plant - genetics; Introns - genetics; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Mutation - genetics; Open Reading Frames - genetics; Phylogeny; Potatoes; Repetitive Sequences, Nucleic Acid - genetics; Sequence Alignment; Sequence Deletion; Sequence Homology, Nucleic Acid; Solanaceae; Solanum bulbocastanum; Solanum tuberosum; Solanum tuberosum - genetics; Indels; Nucleotide sequence; Solanum tuberosum; Chloroplast DNA; Cultivated potato (Solanum tuberosum L. cv. Desiree); Dicotyledones; Angiospermae; Deletion; Chloroplast genome sequence; Spermatophyta; Solanaceae; Genome; Chloroplast; Comparative study; Intergenic region, Open reading frame (ORF)
• ISSN: 0721-7714; 1432-203X
• DOI: 10.1007/s00299-006-0196-4

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.