The distribution of genes in the genomes of Gramineae - PubMed (original) (raw)
The distribution of genes in the genomes of Gramineae
A Barakat et al. Proc Natl Acad Sci U S A. 1997.
Abstract
Recent investigations showed that most maize genes are present in compositional fractions of nuclear DNA that cover only a 1-2% GC (molar fraction of guanosine plus cytosine in DNA) range and represent only 10-20% of the genome. These fractions, which correspond to compositional genome compartments that are distributed on all chromosomes, were collectively called the "gene space." Outside the gene space, the maize genome appears to contain no genes, except for some zein genes and for ribosomal genes. Here, we investigated the distribution of genes in the genomes of two other Gramineae, rice and barley, and used a new set of probes to study further the gene distribution of maize. We found that the distribution of genes in these three genomes is basically similar in that all genes, except for ribosomal genes and some storage protein genes, were located in gene spaces that (i) cover GC ranges of 0.8%, 1.0%, and 1.6% and represent 12%, 17%, and 24% of the genomes of barley, maize, and rice, respectively; (ii) are due to a remarkably uniform base composition in the sequences surrounding the genes, which are now known to consist mainly of transposons; (iii) have sizes approximately proportional to genome sizes, suggesting that expansion-contraction phenomena proceed in parallel in the gene space and in the gene-empty regions of the genome; and (iv) only hybridize on the gene spaces (and not on the other DNA fractions) of other Gramineae.
Figures
Figure 1
Localization of sequences homologous to the BCD855 probe on the _Eco_RI digests of total DNA (lane T) and of Cs2SO4/BAMD fractions from barley. Aliquots of fractions proportional to their representation in 20 μg total DNA were loaded on the gel. Arrows indicate the hybridization bands. The signals on the top of the figure correspond to a nonspecific adsorption of labeled DNA on the pencil marks indicating the wells.
Figure 2
Distribution in a shallow CsCl gradient (14) of nuclear DNA from rice carrying sequences homologous to probe RZ397 (•) and of density markers, the DNA from bacteriophages, λ (○) and T4 (□). The intensities of hybridization signals (left-hand scale) are plotted against the number of fractions collected from the gradient (lower scale). The buoyant density of each fraction (right-hand scale) is represented by a diagonal dashed line in which open triangles correspond to the peak of each DNA.
Figure 3
CsCl profiles of the DNAs from maize, rice, and barley, as obtained by analytical centrifugation of high molecular weight DNA (50–100 kb) in a CsCl density gradient. The gene spaces are indicated by the solid areas. The compartments containing zein genes in the maize genome reach buoyant densities as low as 1.7010 g/cm3 (vertical line). Almost all the probes tested on DNA fractions from barley and rice were localized in the gene space. RZ166 and BCD348 were, however, localized in fractions having buoyant densities of 1.7010 and 1.7012 g/cm3 (vertical lines), respectively, in the DNAs of rice and barley. The arrows indicate the localization of ribosomal genes.
Figure 4
Plot of gene space size vs. genome size for rice, maize, and barley (from the data of Table 3).
Figure 5
Hybridization of labeled gene space fractions from rice on compositional fractions from barley. Other indications are as in Fig. 3.
References
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- Mouchiroud D, D’Onofrio G, Aissani B, Macaya G, Gautier C, Bernardi G. Gene. 1990;100:181–187. - PubMed
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