Complete chloroplast genome sequences of Hordeum vulgare , Sorghum bicolor and Agrostis stolonifera.pdf

Theor Appl Genet (2007) 115:571–590 DOI 10.1007/s00122-007-0567-4 ORIGINAL PAPER Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes Christopher Saski · Seung-Bum Lee · Siri Fjellheim · Chittibabu Guda · Robert K. Jansen · Hong Luo · JeVrey Tomkins · Odd Arne Rognli · Henry Daniell · Jihong Liu Clarke Received: 22 November 2006 / Accepted: 23 April 2007 / Published online: 30 May 2007 ? Springer-Verlag 2007 Abstract 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 dupli- cates 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 19- 37 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 poly- morphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum oYcinarum and Sor- ghum 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-c