Variations in a hotspot region of chloroplast DNAs among common wheat and Aegilops revealed by nucleotide sequence analysis

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The second largest <i>Bam</i>HI fragment (B2) of the chloroplast DNA in <i>Triticum</i> (wheat) and <i>Aegilops</i> contains a highly variable region (a hotspot), resulting in four types of B2 of different size, i.e. B2l (10.5kb), B2m (10.2kb), B2 (9.6kb) and B2s (9.4kb). In order to gain a better understanding of the molecular nature of the variations in length and explain unexpected identity among B2 of <i>Ae. ovata</i>, <i>Ae. speltoides </i>and common wheat (<i>T. aestivum</i>), the nucleotide sequence between a stop codon of <i>rbcL</i> and a <i>Hin</i>dIII site in <i>cemA</i> in the hotspot was determined for <i>Ae. ovata</i>, <i>Ae. speltoides, Ae. caudata</i> and <i>Ae. mutica. </i>The total number of nucleotides in the region was 2808, 2810, 3302, and 3594 bp, for <i>Ae. speltoides</i>, <i>Ae. ovata</i>, <i>Ae. caudata</i> and <i>Ae. mutica, </i>respectively, and the sequences were compared with the corresponding ones of <i>Ae. crassa</i> 4x, <i>T. aestivum</i> and <i>Ae. squarrosa</i>. Compared with the largest B2l fragment of <i>Ae. mutica</i>, a 791bp and a 793 bp deletion were found in <i>Ae. speltoides</i> and <i>Ae. ovata, </i>respectively, and the possible site of deletion in the two species is the same as that of <i>T. aestivum. </i>However, a deleted segment in <i>Ae. ovata</i> is 2 bp longer than that of <i>Ae. speltoides</i> (and <i>T. aestivum</i>), demonstrating that recurrent deletions had occurred in the chloroplast genomes of both species. Comparison of the sequences from <i>Ae. caudata</i> and <i>Ae. crassa</i> 4x with that of <i>Ae. mutica</i> revealed a 289 bp and a 61 bp deletion at the same site in <i>Ae. caudata</i> and <i>Ae. crassa</i> 4x, respectively. Sequence comparison using wild <i>Aegilops</i> plants showed that the large length variations in a hotspot are fixed to each species. A considerable number of polymorphisms are observed in a loop in the 3' of <i>rbcL</i>. The study reveals the relative importance of the large and small indels and minute inversions to account for variations in the chloroplast genomes among closely related species.<br>


  • The Japanese Journal of Genetics  

    The Japanese Journal of Genetics 80(4), 277-285, 2005-08-25 

    The Genetics Society of Japan

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