Plant Cell Rep (2006) 25: 1369–1379 DOI 10.1007/s00299-006-0196-4 GENETICS AND GENOMICS Hwa-Jee Chung · Jong Duk Jung · Hyun-Woo Park · Joo-Hwan Kim · Hyun Wook Cha · Sung Ran Min · Won-Joong Jeong · Jang Ryol Liu 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 Received: 14 April 2006 / Revised: 29 May 2006 / Accepted: 9 June 2006 / Published online: 12 July 2006 C  Springer-Verlag 2006 Abstract The complete nucleotide sequence of the chloro- plast 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 re- gions of 18,373 and 85,749 bp, respectively. The genome contains 79 proteins, 30 tRNAs, 4 rRNAs, and unidenti- fied 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 read- ing frames (ORFs) in LSC region were highly diverged in Solanaceae species except N. sylvestris. Detailed com- parison was identified by numerous indels in the inter- genic regions that were mostly located in the LSC region. Among them, a single large 241-bp deletion, was not asso- ciated with direct repeats and found in only S. tuberosum, Communicated by I. S. Chung H.-J. Chung · H. W. Cha · S. R. Min · W.-J. Jeong · J. R. Liu () Plant Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-333, Korea e-mail: jrliu@kribb.re.kr Fax: +82-42-860-4608 e-mail: hwajee@kribb.re.kr e-mail: hwcha@kribb.re.kr e-mail: srmin@kribb.re.kr e-mail: wonjoong@kribb.re.kr J. D. Jung · H.-W. Park Laboratory of Functional Genomics for Plant Secondary Metabolism, Eugentech Inc., Daejeon 305-333, Korea e-mail: seq1@eugentech.com e-mail: dnahyun@eugentech.com J.-H. Kim Department of Life Science, Daejeon University, Daejeon 300-716, Korea e-mail: kimjh@dju.ac.kr clearly discriminates a cultivated potato from wild potato species Solanum bulbocastanum. The extent of sequence divergence may provide the basis for evaluating genetic di- versity 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) Introduction Chloroplasts are intracellular organelles that have their own genome in which a number of genes are encoded for the chloroplast components and photosynthesis. Chloroplast genomes vary in size from 35 to 217 kb, but in land plants, most of them are between 115 and 165 kb and exhibit a high similarity in their structure and gene organization (Jansen et al. 2005). The overall structure of chloroplast genome consists of two copies of an inverted repeat (IR) ranging from 5 to 76 kb in length. These copies are separated by a large single-copy (LSC) and a small single-copy (SSC) region (Sugiura et al. 1998). Although the overall structure of the chloroplast is relatively uniform and is conserved in land plants, a number of mutations have been observed in the chloroplast genome. The mutations include structural changes such as inversions (Kim et al. 2005; Kim and Lee 2005; Sugiura et al. 2003), rearrangements of gene order (Cosner et al. 2004; Saski et al. 2005), and insertions/deletions (indels) (Calsa Junior et al. 2004; Kato et al. 2000; Ogihara et al. 2002; Shahid Masood et al. 2004) as well as base substitutions (Schmitz-Linneweber et al. 2002). A comparison of the complete chloroplast sequences of the closely related grass family, maize, wheat, rice, and sugarcane, reveals the presence of several hotspots for length mutations (Asano et al. 2004; Calsa Junior et al.