Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 May 25;16(10):4269–4285. doi: 10.1093/nar/16.10.4269

Compositional compartmentalization and compositional patterns in the nuclear genomes of plants.

J Salinas 1, G Matassi 1, L M Montero 1, G Bernardi 1
PMCID: PMC336629  PMID: 3380684

Abstract

We report here results which indicate (i) that the nuclear genomes of angiosperms is characterized by a compositional compartmentalization and an isochore structure; and (ii) that the nuclear genomes of some Gramineae exhibit strikingly different compositional patterns compared to those of many dicots. Indeed, the compositional distribution of nuclear DNA molecules (in the 50-100 Kb size range) from three dicots (pea, sunflower and tobacco) and three monocots (maize, rice and wheat) were found to be centered around lower (41%) and higher (45% for rice, 48% for maize and wheat) GC levels, respectively (and to trail towards even higher GC values in maize and wheat). Experiments on gene localization in density gradient fractions showed a remarkable compositional homogeneity in vast (greater than 100-200 Kb) regions surrounding the genes. On the other hand, the compositional distribution of coding sequences (GenBank and literature data) from dicots (several orders) was found to be narrow, symmetrical and centered around 46% GC, that from monocots (essentially barley, maize and wheat) to be broad, asymmetrical and characterized by an upward trend towards high GC values, with the majority of sequences between 60 and 70% GC. Introns exhibited a similar compositional distribution, but lower GC levels, compared to exons from the same genes.

Full text

PDF
4270

Images in this article

4279Image
on p.4279

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bernardi G., Bernardi G. Compositional constraints and genome evolution. J Mol Evol. 1986;24(1-2):1–11. doi: 10.1007/BF02099946. [DOI] [PubMed] [Google Scholar]
  2. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 1985 May 24;228(4702):953–958. doi: 10.1126/science.4001930. [DOI] [PubMed] [Google Scholar]
  3. Cortadas J., Macaya G., Bernardi G. An analysis of the bovine genome by density gradient centrifugation: fractionation in Cs2SO4/3,6-bis(acetatomercurimethyl)dioxane density gradient. Eur J Biochem. 1977 Jun 1;76(1):13–19. doi: 10.1111/j.1432-1033.1977.tb11565.x. [DOI] [PubMed] [Google Scholar]
  4. Forde J., Malpica J. M., Halford N. G., Shewry P. R., Anderson O. D., Greene F. C., Miflin B. J. The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.). Nucleic Acids Res. 1985 Oct 11;13(19):6817–6832. doi: 10.1093/nar/13.19.6817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gouy M., Milleret F., Mugnier C., Jacobzone M., Gautier C. ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):121–127. doi: 10.1093/nar/12.1part1.121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Huguet T., Jouanin L. The heterogeneity of wheat nuclear DNA. Biochim Biophys Acta. 1972 Apr 12;262(4):431–440. doi: 10.1016/0005-2787(72)90486-8. [DOI] [PubMed] [Google Scholar]
  7. Ingle J., Pearson G. G., Sinclair J. Species distribution and properties of nuclear satellite DNA in higher plants. Nat New Biol. 1973 Apr 18;242(120):193–197. doi: 10.1038/newbio242193a0. [DOI] [PubMed] [Google Scholar]
  8. Kemp J. D., Sutton D. W. A chemical and physical method for determining the complete base composition of plant DNA. Biochim Biophys Acta. 1976 Mar 4;425(2):148–156. doi: 10.1016/0005-2787(76)90020-4. [DOI] [PubMed] [Google Scholar]
  9. Kirk J. T. Effect of methylation of cytosine residues on the buoyant density of DNA in caesium chloride solution. J Mol Biol. 1967 Aug 28;28(1):171–172. doi: 10.1016/s0022-2836(67)80087-1. [DOI] [PubMed] [Google Scholar]
  10. Kislev N., Rubenstein I. Utility of ethidium bromide in the extraction from whole plants of high molecular weight maize DNA. Plant Physiol. 1980 Dec;66(6):1140–1143. doi: 10.1104/pp.66.6.1140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lamppa G. K., Morelli G., Chua N. H. Structure and developmental regulation of a wheat gene encoding the major chlorophyll a/b-binding polypeptide. Mol Cell Biol. 1985 Jun;5(6):1370–1378. doi: 10.1128/mcb.5.6.1370. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Mouchiroud D., Fichant G., Bernardi G. Compositional compartmentalization and gene composition in the genome of vertebrates. J Mol Evol. 1987;26(3):198–204. doi: 10.1007/BF02099852. [DOI] [PubMed] [Google Scholar]
  13. Salinas J., Zerial M., Filipski J., Bernardi G. Gene distribution and nucleotide sequence organization in the mouse genome. Eur J Biochem. 1986 Nov 3;160(3):469–478. doi: 10.1111/j.1432-1033.1986.tb10063.x. [DOI] [PubMed] [Google Scholar]
  14. Sorenson J. C. The structure and expression of nuclear genes in higher plants. Adv Genet. 1984;22:109–144. doi: 10.1016/s0065-2660(08)60039-5. [DOI] [PubMed] [Google Scholar]
  15. Wagner I., Capesius I. Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography. Biochim Biophys Acta. 1981 Jun 26;654(1):52–56. doi: 10.1016/0005-2787(81)90135-0. [DOI] [PubMed] [Google Scholar]
  16. Zerial M., Salinas J., Filipski J., Bernardi G. Gene distribution and nucleotide sequence organization in the human genome. Eur J Biochem. 1986 Nov 3;160(3):479–485. doi: 10.1111/j.1432-1033.1986.tb10064.x. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES