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Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5 end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identiWed 1937 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identiWed 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum oYcinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identiWed six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood Communicated by A. Paterson. Electronic supplementary material The online version of this article (doi:10.1007/s00122-007-0567-4) contains supplementary material, which is available to authorized users. C. Saski · J. Tomkins Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51 New Cherry Street, Clemson, SC 29634, USA S.-B. Lee · H. Daniell (&) 4000 Central Florida Blvd, Department of Molecular Biology and Microbiology, Biomolecular Science, University of Central Florida, Building #20, Orlando, FL 32816-2364, USA e-mail: daniell@mail.ucf.edu S. Fjellheim · O. A. Rognli Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, 1432 Aas, Norway C. Guda Gen*NY*Sis Center for Excellence in Cancer Genomics and Department of Epidemiology and Biostatistics, State University of New York at Albany, 1 Discovery Dr Rensselaer, New York, NY 12144, USA R. K. Jansen Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA H. Luo Department of Genetics and Biochemistry, Clemson University, 51 New Cherry Street, Clemson, SC 29634, USA J. L. Clarke Department of Genetics and Biotechnology, Norwegian Institute for Agricultural and Environmental Sciences, 1432 Aas, Norway

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes