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

    Authors

    C. Saski; S. B. Lee; S. Fjellheim; C. Guda; R. K. Jansen; H. Luo; J. Tomkins; O. A. Rognli; H. Daniell;J. L. Clarke

    Comments

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    Abbreviated Journal Title

    Theor. Appl. Genet.

    Keywords

    COMPLETE NUCLEOTIDE-SEQUENCE; TRANSFER-RNA GENES; TOBACCO CHLOROPLASTS; TRANSGENIC CHLOROPLASTS; PLASTID CHROMOSOME; BASAL ANGIOSPERM; PHYLOGENETIC-RELATIONSHIPS; CREEPING BENTGRASS; PROTECTIVE ANTIGEN; NICOTIANA-TABACUM; Agronomy; Plant Sciences; Genetics & Heredity; Horticulture

    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 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 identified 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) identified 16-21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum 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 identified 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 methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.

    Journal Title

    Theoretical and Applied Genetics

    Volume

    115

    Issue/Number

    4

    Publication Date

    1-1-2007

    Document Type

    Review

    Language

    English

    First Page

    571

    Last Page

    590

    WOS Identifier

    WOS:000249207100013

    ISSN

    0040-5752

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