Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates

Abstract

We have hybridized a human DNA fraction corresponding to the GC-richest and gene-richest isochore family, H3, on compositional fractions of DNAs from 12 mammalian species and three avian species, representing eight and three orders, respectively. Under conditions in which repetitive sequences are competed out, the H3 isochore probe only or predominantly hybridized on the GC-richest fractions of main-band DNA from all the species investigated. These results indicate that single-copy sequences from the human H3 isochores share homology with sequences located in the compositionally corresponding compartments of the vertebrate genomes tested. These sequences are likely to be essentially formed by conserved coding sequences. The present results add to other lines of evidence indicating that isochore patterns are highly conserved in warm-blooded vertebrate genomes. Moreover, they refine recent reports (Sabeur et al., 1993; Kadi et al., 1993), and correct them in some details and also in demonstrating that the shrew genome does not exhibit the general mammalian pattern, but a special pattern.

Diversity and Phylogenetic Implications of CsCl Profiles from Rodent DNAs

“…The distribution of genes found in human is similar to those in other nonrodent mammals, whereas the murids so far studied are characterized by reduced CsCl profile (main band) skewness, a relative absence of very GC-rich DNA having Ͼ 1.710 g/cm 3 , and a shift of the GC-richest genes toward GC-poorer DNA, called the minor shift (see Bernardi et al, 1995 and references therein). This compositional shift of genes can be seen as a shift in slot blot hybridization patterns: the GC-richest gene-containing DNA of rodents, which can be identified by hybridization with the GCrichest gene-containing DNA of human (H3), is located in GC-rich fractions in squirrel and guinea pig (nonMuridae), but in GC-poorer fractions in mouse and mole rat (Muridae) (Cacciò et al, 1994).…”

Base Compositional Bias and Phylogenetic Analyses: A Test of the “Flying DNA” Hypothesis

“…Because there is considerable heterogeneity in base composition among mammalian nuclear genomes (Bernardi et al, 1985(Bernardi et al, , 1988Bernardi, 1993;Mouchiroud and Bernardi, 1993;Sabeur et al, 1993;Cacciò et al, 1994), the relevant issue for molecular systematic studies is the base composition in the segments of DNA that have been sequenced and analyzed for a given set of taxa. Several nuclear and mitochondrial genes from diverse mammalian taxa have been sequenced and Table 1 presents data on nucleotide composition of the five genes under study for representatives of the eutherian orders that were available via GenBank.…”

Gene-rich and gene-poor chromosomal regions have different locations in the interphase nuclei of cold-blooded vertebrates

“…In the case of cold-blooded vertebrates, evidence is available for a bimodal distribution of genes, but GC-rich isochores have a much lower GC level than in warmblooded vertebrates (Cacciò et al 1994;Jabbari and Bernardi 2004; for a review, see Bernardi 2004). In the present work, we investigated the distribution of genes from cold-blooded vertebrates by hybridizing the well-characterized gene-poor and gene-rich isochores of chicken Cortadas et al 1979;Olofsson and Bernardi 1983;Kadi et al 1993;Smith et al 2000;McQueen et al 1996;Andreozzi et al 2001;Habermann et al 2001;Saccone et al 2002; for review, see Bernardi 2004) on chromosomes and nuclei from the lizard Podarcis sicula and the frog Rana esculenta.…”