Structure and sequence evolution of three legume chloroplast DNAs

Abstract

Chloroplast DNAs from soybean (Glycine max), common bean (Phaseolus vulgaris) and mung bean (Vigna radiata) have been compared in overall structure and nucleotide sequence homologies. Detailed restriction maps demonstrate that the soybean and common bean genomes possess the classical large chloroplast DNA inverted repeat, encoding ribosomal RNA genes, as found previously in mung bean (Palmer and Thompson 1981 a). Heterologous filter hybridizations indicate essentially complete colinearity between mung bean and common bean chloroplast DNAs. Although the linear order of sequence elements is also conserved between soybean and mung bean DNAs, two regions of deletions/additions, each totaling almost 5 kilobase pairs in size, have been identified at the ends of the large single copy DNA region. Alignment and comparison of restriction maps has allowed calculation of nucleotide sequence divergence values for the three DNAs. Mung bean and soybean chloroplast DNAs differ by an average of 10–13% in nucleotide sequence, while mung bean and common bean are significantly more closely related, differing by only 5–6% in base sequence. Base substitutions are distributed non-randomly in these chloroplast DNAs; chloroplast ribosomal DNA is relatively conserved and the two deletion/addition regions relatively diverged in base sequence.