The second largest
BamHI fragment (B2) of the chloroplast DNA in
Triticum (wheat) and
Aegilops 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
Ae. ovata,
Ae. speltoides and common wheat (
T. aestivum), the nucleotide sequence between a stop codon of
rbcL and a
HindIII site in
cemA in the hotspot was determined for
Ae. ovata,
Ae. speltoides, Ae. caudata and
Ae. mutica. The total number of nucleotides in the region was 2808, 2810, 3302, and 3594 bp, for
Ae. speltoides,
Ae. ovata,
Ae. caudata and
Ae. mutica, respectively, and the sequences were compared with the corresponding ones of
Ae. crassa 4x,
T. aestivum and
Ae. squarrosa. Compared with the largest B2l fragment of
Ae. mutica, a 791bp and a 793 bp deletion were found in
Ae. speltoides and
Ae. ovata, respectively, and the possible site of deletion in the two species is the same as that of
T. aestivum. However, a deleted segment in
Ae. ovata is 2 bp longer than that of
Ae. speltoides (and
T. aestivum), demonstrating that recurrent deletions had occurred in the chloroplast genomes of both species. Comparison of the sequences from
Ae. caudata and
Ae. crassa 4x with that of
Ae. mutica revealed a 289 bp and a 61 bp deletion at the same site in
Ae. caudata and
Ae. crassa 4x, respectively. Sequence comparison using wild
Aegilops 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
rbcL. 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.
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