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

    Authors

    H. Daniell; S. B. Lee; J. Grevich; C. Saski; T. Quesada-Vargas; C. Guda; J. Tomkins;R. K. Jansen

    Comments

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    Abbreviated Journal Title

    Theor. Appl. Genet.

    Keywords

    COMPLETE NUCLEOTIDE-SEQUENCE; RNA EDITING SITES; TOBACCO CHLOROPLASTS; TRANSGENIC CHLOROPLASTS; PLASTID CHROMOSOME; INVERTED REPEAT; EVOLUTIONARY SIGNIFICANCE; MULTIPLE INVERSIONS; PROTECTIVE ANTIGEN; NICOTIANA-TABACUM; Agronomy; Plant Sciences; Genetics & Heredity; Horticulture

    Abstract

    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 significant 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 identified 33-45 direct and inverted repeats > = 30 bp with a sequence identity of at least 90%; all but five 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 first 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.

    Journal Title

    Theoretical and Applied Genetics

    Volume

    112

    Issue/Number

    8

    Publication Date

    1-1-2006

    Document Type

    Article

    Language

    English

    First Page

    1503

    Last Page

    1518

    WOS Identifier

    WOS:000237509700013

    ISSN

    0040-5752

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