Nucleic Acids Research, 1990, Vol. 18, No. 7 1859-1867
© 1990
GENOME STRUCTURE AND MAPPING |
Gene distribution and isochore organization in the nuclear genome of plants
Departamento de Proteccion Vegetal, Instituto Nacional de Investigaciones Agrarias Carretera de La Coruna, Km 7, 28040 Madrid, Spain 1Laboratoire de Génétique Moléculaire, Institut Jacques Monod 2 Place Jussieu, 75005 Paris, France
Received September 29, 1989. Revised January 3, 1990. Accepted January 3, 1990.
The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of these genes (and of many other related genes and pseudogenes) was found to be located in DNA fragments (50–100 Kb in size) that were less than 1–2% GC apart from each other. This definitively demonstrates the existence of isochores in plant genomes, namely of compositionally homogeneous DNA regions at least 100–200 Kb in size. Moreover, the GC levels of the 23 coding sequences studied, of their first, second and third codon positions, and of the corresponding introns were found to be linearly correlated with the GC levels of the isochores harboring those genes. Compositional correlations displayed increasing slopes when going from second to first to third codon position with obvious effects on codon usage. Coding sequences for seed storage proteins and phytochrome of Gramineae deviate from the compositional correlations just described. Finally, CpG doublets of coding sequences were characterized by a shortage that decreased and vanished with increasing GC levels of the sequences. A number of these findings bear a striking similarity with results previously obtained for vertebrate genes (1, 2).
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