The chloroplast genomes of azuki bean and its close relatives: a deletion mutation found in weed azuki bean

A physical map of the azuki bean (Vigna angularis cv. Erimo-shozu) chloroplast DNA (cpDNA) was constructed by localising the cleavage sites of PstI, SalI, SmaI, SacI, KpnI, PvuII and XhoI. The resulting map is more similar to the cpDNA-maps of two Vigna species (mung bean, V. radiata, and V. nakashimae) than to common bean (Phaseolus vulgaris) cpDNA map. Azuki bean was originally classified in the genus Phaseolus, and the inclusion of this taxon in the genus Vigna is a recent taxonomic decision. Our result is thus in favour of the taxonomic placement of azuki bean in the same genus as V. nakashimae and mung bean. We also found that a weed-form accession of azuki bean has a 96-bp deletion relative to the cultivar Erimo-shozu. The 96-bp deletion is located between the trnS-UGA and psbC genes in the large single-copy region of the chloroplast genome. This deletion is flanked by imperfect 9-bp direct repeats, suggesting that the deletion was a result of intra-molecular recombination mediated by these direct repeats.