The isochore patterns of mammalian genomes and their phylogenetic implications

Abstract

The compositional distributions of high molecular weight DNA fragments from 20 species belonging to 9 out of the 17 eutherian orders were investigated by analytical CsCl density gradient centrifugation and by preparative fractionation in Cs2SO4/BAMD density gradients followed by analysis of the fractions in CsCl. These compositional distributions reflect those of the isochores making up the corresponding genomes. A "general distribution" was found in species belonging to eight mammalian orders. A "myomorph distribution" was found in Myomorpha, but not in the other rodent infraorders Sciuromorpha and Histricomorpha, which share the general distribution. Two other distributions were found in a megachiropteran (but not in microchiropteran, which, again, shares the general distribution) and in pangolin (a species from the only genus of the order Pholidota), respectively. The main difference between the general distribution and all other distributions is that the former contains sizable amounts (6-10%) of GC-rich isochores (detected as DNA fragments equal to, or higher than, 1.710 g/cm3 in modal buoyant density), which are scarce, or absent, in the other distributions. This difference is remarkable because gene concentrations in mammalian genomes are paralleled by GC levels, the highest gene concentrations being present in the GC-richest isochores. The compositional distributions of mammalian genomes reported here shed light on mammalian phylogeny. Indeed, all orders investigated, with the exception of Pholidota, seem to share a common ancestor. The compositional patterns of the megachiropteran and of Myomorpha may be derived from the general pattern or have independent origins.

The Organization and Rate of Evolution of Wheat Genomes Are Correlated With Recombination Rates Along Chromosome Arms

“…This is consistent with other lines of evidence suggesting that the chromosomes of most plants and animals are subdivided into gene-rich and gene-poor isochors (Sabeur et al 1993;Bernardi 1996;Barakat et al 1997;Bernardi et al 1997;Carels et al 1998;Bernardi 1999).…”

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

“…Pettigrew's (1994) main argument for the ''flying DNA'' hypothesis is that bats contain a higher percentage of A and T in their genomes than do other mammals. Pettigrew (1994) cited data on the base composition of the entire nuclear genome presented by Sabeur et al, (1993) in support of this conclusion. However, examination of the Sabeur et al (1993) data indicates that the bat genomes (based on single representatives of Megachiroptera and Microchiroptera) do not have elevated levels of A and T relative to the single representative of Primates (Fig.…”

“…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.…”

Lineage-Specific Evolutionary Rate in Mammalian mtDNA

“…Such an interaction could not be restricted only to the genes for the respiratory chain and could be even stronger for mitochondrial processes that are completely dependent on nuclear genes, such as DNA replication. Furthermore, this coevolutionary process could operate in a taxon-specific manner, as it is known that the isochore structure of the nuclear genome shows taxon-specific features (Sabeur et al 1993). Thus, the pattern of rate heterogeneity between taxa found at the mitochondrial level should also be investigated at the nuclear level.…”