Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Henry Daniell, Seung Bum Lee, Justin Grevich, Christopher Saski, Tania Quesada-Vargas, Chittibabu Guda, Jeffrey Tomkins, Robert K. Jansen

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Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals signiWcant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identiWed 33-45 direct and inverted repeats ≥30 bp with a sequence identity of at least 90%; all but Wve of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the Wrst time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato.

Original languageEnglish (US)
Pages (from-to)1503-1518
Number of pages16
JournalTheoretical and Applied Genetics
Issue number8
Publication statusPublished - May 1 2006


ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

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