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Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

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Abstract

Tomato, Solanum lycopersicum (formerly Lycopersicon esculentum), has long been one of the classical model species of plant genetics. More recently, solanaceous species have become a model of evolutionary genomics, with several EST projects and a tomato genome project having been initiated. As a first contribution toward deciphering the genetic information of tomato, we present here the complete sequence of the tomato chloroplast genome (plastome). The size of this circular genome is 155,461 base pairs (bp), with an average AT content of 62.14%. It contains 114 genes and conserved open reading frames (ycfs). Comparison with the previously sequenced plastid DNAs of Nicotiana tabacum and Atropa belladonna reveals patterns of plastid genome evolution in the Solanaceae family and identifies varying degrees of conservation of individual plastid genes. In addition, we discovered several new sites of RNA editing by cytidine-to-uridine conversion. A detailed comparison of editing patterns in the three solanaceous species highlights the dynamics of RNA editing site evolution in chloroplasts. To assess the level of intraspecific plastome variation in tomato, the plastome of a second tomato cultivar was sequenced. Comparison of the two genotypes (IPA-6, bred in South America, and Ailsa Craig, bred in Europe) revealed no nucleotide differences, suggesting that the plastomes of modern tomato cultivars display very little, if any, sequence variation.

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Acknowledgments

We thank the MPI-MP Green Team for plant care and cultivation, Andy Phillips for gifts of cloned fragments of the Ailsa Craig plastome, Graham Seymour for details on the origin of Ailsa Craig, and Helaine Carrer (University of São Paulo, Brazil) for obtaining information on the origin of IPA-6. This research was supported by a collaborative grant from the European Union (FP6 Plastomics Project LSHG-CT-2003-503238) to J.C.G. and R.B. and by the Max Planck Society.

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  1. Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm, D-14476, Germany

    Sabine Kahlau & Ralph Bock

  2. Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK

    Sue Aspinall & John C. Gray

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  1. Sabine Kahlau
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  2. Sue Aspinall
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  3. John C. Gray
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  4. Ralph Bock
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Correspondence to Ralph Bock.

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Kahlau, S., Aspinall, S., Gray, J.C. et al. Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes. J Mol Evol 63, 194–207 (2006). https://doi.org/10.1007/s00239-005-0254-5

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