Summary
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.
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Abbreviations
- kb:
-
kilobase pairs
- bp:
-
base pairs
- rDNA:
-
ribosomal DNA
- rRNA:
-
ribosomal RNA
References
Bell EA, Lackey JA, Polhill RM (1978) Systematic significance of canavanine in the papilionoideae (faboideae). Biochem Syst Ecol 6:201–212
Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513–1523
Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76:1967–1971
Brown GG, Simpson MV (1981) Intra-and interspecific variation of the mitochondrial genome in Rattus norvegicus and Rattus rattus: Restriction enzyme analysis of variant mitochondrial DNA molecules and their evolutionary relationships. Genetics 97:125–143
Chu NM, Tewari KK (1982) Arrangement of the ribosomal RNA genes in chloroplast DNA of Leguminosae. Mol Gen Genet 186:23–32
Driesel AJ, Crouse EJ, Gordon K, Bohnert HJ, Herrmann RG, Steinmetz A, Mubumbila M, Keller M, Burkard G, Weil JH (1979) Fractionation and identification of spinach chloroplast transfer RNAs and mapping of their genes on the restriction map of chloroplast DNA. Gene 6:285–306
Ellis RJ, Highfield PE, Silverthorne J (1977) The synthesis of chloroplast proteins by subcellular systems. Proceedings of the 4th International Congress on Photosynthesis. Elsevier/North-Holland, Amsterdam, pp 497–503
Ferris SD, Brown WM, Davidson WS, Wilson AC (1981) Extensive polymorphism in the mitochondrial DNA of apes. Proc Natl Acad Sci USA 78:6319–6323
Fluhr R, Edelman M (1981 b) Conservation of sequence arrangement among higher plant chloroplast DNAs: Molecular cross hybridization among the Solanaceae and between Nicotiana and Spinacia. Nucl Acids Res 9:6841–6853
Gillham NW, Boynton JE and Harris EH (1982) Evolution of plastid DNA. In: Cavalier-Smith T (ed) DNA evolution: Natural selection and genome size. John Wiley and Sons, New York
Gordon KHJ, Crouse EJ, Bohnert HJ, Herrmann RG (1982) Physical mapping of differences in chloroplast DNA of the five wild-type plastomes in Oenothera subsection Euenothera. Theor Appl Genet 61:373–384
Kolodner R, Tewari KK (1975) The molecular size and conformation of the chloroplast DNA from higher plants. Biochim Biophys Acta 402:372–390
Kolodner R, Tewari KK (1979) Inverted repeats in chloroplast DNA from higher plants. Proc Natl Acad Sci USA 76:41–45
Lamppa GK, Bendich AJ (1981) Fine scale interspersion of conserved sequences in the pea and corn chloroplast genomes. Mol Gen Genet 182:310–320
Maizels N (1976) Dictyostelium 17S, 25S, and 5S rDNA lie within a 38,000 base pair repeated unit. Cell 9:431–438
Maniatis T, Jeffrey A, Klein DG (1975) Nucleotide sequence of the rightward operator of phage λ. Proc Natl Acad Sci USA 72:1184–1188
Meeker R, Tewari KK (1980) Transfer RNA genes in the chloroplast deoxyribonucleic acid of pea leaves. Biochem 19:5973–5981
Mubumbila M, Gordon K, Crouse EJ, Burkard G, Weil JH (1983) Construction of the physical map of the chloroplast DNA of Phaseolus vulgaris and localization of ribosomal and transfer RNA genes. Gene (submitted)
Oishi K, Sumnicht T, Tewari KK (1981) Messenger ribonucleic acid transcripts of pea chloroplast deoxyribonucleic acid. Biochem 20:5710–5717
Palmer JD (1982) Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativa. Nucleic Acids Res 10:1593–1605
Palmer JD (1983) Chloroplast DNA exists in two orientations. Nature 301:92–93
Palmer JD, Thompson WF (1981 a) Rearrangements in the chloroplast genomes of mung bean and pea. Proc Natl Acad Sci USA 78:5533–5537
Palmer JD, Thompson WF (1981 b) Clone banks of the mung bean, pea and spinach chloroplast genomes. Gene 15:21–26
Palmer JD, Thompson WF (1982) Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell 29:537–550
Palmer JD, Stein DB (1982) Chloroplast DNA from the fern Osmunda cinnamomea: Physical organization, gene localization and comparison to angiosperm chloroplast DNA. Current Genet 5:165–170
Palmer JD, Zamir D (1982) Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci USA 79:5006–5010
Palmer JD, Edwards H, Jorgensen RA, Thompson WF (1982) Novel evolutionary variation in transcription and location of two chloroplast genes. Nucleic Acids Res (in press)
Polhill RM, Raven PH (1981) Advances in legume systematics, proceedings of the International Legume Conference. Royal Botanic Gardens, Kew, England, pp 1–1049
Singh GP, Palmer JD, Pillay DTN (1982) A map of specific cleavage sites and rRNA genes in the chloroplast genome of soybean (Glycine max L). Plant Physiol 69:20a
Takaiwa F, Sugiura M (1982) The complete nucleotide sequence of a 23S rRNA gene from tobacco chloroplasts. Eur J Biochem 124:13–19
Thomas JR, Tewari KK (1974) Conservation of 70S ribosomal RNA genes in the chloroplast DNAs of higher plants. Proc Natl Acad Sci USA 71:3147–3151
Tohdoh N, Sugiura M (1982) The complete nucleotide sequence of a 16S ribosomal RNA gene from tobacco chloroplasts. Gene 17:213–218
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Communicated by J. Schell
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Palmer, J.D., Singh, G.P. & Pillay, D.T.N. Structure and sequence evolution of three legume chloroplast DNAs. Mol Gen Genet 190, 13–19 (1983). https://doi.org/10.1007/BF00330318
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DOI: https://doi.org/10.1007/BF00330318