Isochore pattern and gene distribution in the chicken genome

Abstract

We report here investigations on the isochore pattern and the distribution of genes in the chromosomes of chicken. In spite of large differences in genome size and karyotype, the compositional properties and the gene distribution of the chicken genome are very similar to those recently published for the human genome, which is a good representative of most mammalian genomes. In fact, this similarity, which extends to the relative amounts and, also, to a large extent at least, to the average base composition of isochore families, is most interesting in view of the very large distance of mammals and birds for a common ancestor, which goes back to 310–340 million years ago. This raises important questions about genome evolution in vertebrates.

Introduction

The first compositional analysis of avian genomes was obtained by ultracentrifugation in CsCl density gradients (Thiery et al., 1976). Both avian DNAs investigated, from chicken and sea-gull, showed compositional patterns that were remarkably similar to those of mammalian DNAs. A much more detailed analysis (Cortadas et al., 1979) of chicken DNA using preparative Cs₂SO⁴/Ag⁺ and Cs₂SO₄/BAMD (BAMD is 3,6-bis(acetato–mercury–methyl)dioxane) revealed that 88% of the chicken genome was made up of four “major DNA components”, DNA fractions that were similar in relative amounts and base composition to those of mammalian genomes. The demonstration of the compositional homogeneity over at least 200 kb around the ovalbumin gene (Cortadas et al., 1979) indicated that the DNA molecules (about 100 kb in size) forming the major components derived from much longer, fairly homogeneous chromosomal regions previously identified in mammalian genomes, the isochores (Macaya et al., 1976). In other words, the chicken genome, like the mammalian genome, was a mosaic of isochores that belonged to four major families, which were called L1, L2, H1, and H2 because of their similarity with the corresponding isochore families of mammals. The remaining 12% of the genome was formed by seven minor and/or satellite components, two of which were later identified as derived from two additional isochore families, H3 (Bernardi et al., 1985) and H4 (Bernardi, 1989). While the H3 family was also present in the mammalian genome, the H4 family was only present in chicken (and other avian genomes; see below).

Further work showed (i) that the relative amounts of interspersed repeats were different in different chicken isochores and different from those of the corresponding mammalian isochores (Olofsson and Bernardi, 1983a, Olofsson and Bernardi, 1983b); and (ii) that the compositional patterns of the genomes of birds belonging to eight different orders (both paleognathous and neognathous) were very similar, as were orthologous coding sequences (Kadi et al., 1993). Moreover, a remarkable compositional similarity was found for orthologous genes from human and chicken, especially in the case of GC-poor genes (see Bernardi et al., 1997). Another aspect of the similarity of avian and mammalian genomes concerned their lower CpG and mC levels compared to those of fishes/amphibians (Jabbari et al., 1997, Cacciò et al., 1994, Varriale and Bernardi, 2006).

An analysis of GC₃ levels and codon frequencies of genes from human, chicken and Xenopus (Cruvellier et al., 2000) showed that GC-poor genes were characterized by only minor differences in orthologous sets from Xenopus, human and chicken, a remarkable result in view of the very many nucleotide substitutions that occurred over the long evolutionary times separating these species from their common ancestor. In contrast, GC-rich genes showed large differences between Xenopus and warm-blooded vertebrates, but only relatively small differences between chicken and human, the independent changes that occurred in avian and mammalian genes being similar in average composition.

Along a different line, the experimental assessment of the GC level of the chromosomal bands, led to the identification in human chromosomes of the GC-richest and of the GC-poorest bands, which were predominantly localized in telomeres and in internal regions, respectively (see Saccone et al., 1992, Saccone et al., 1993). The same approach (Andreozzi et al., 2001) showed that the GC-richest isochores of chicken are localized not only on a large number of microchromosomes in agreement with previous findings on the concentration of CpG islands and genes on microchromosomes (McQeen et al., 1996, McQueen et al., 1998), but also on almost all telomeric bands of macrochromosomes. On the other hand, the GC-poorest isochores are generally localized in the internal regions of macrochromosomes and are almost absent in microchromosomes. Interestingly, in the Accipitridae (diurnal raptors), an avian family that shows no very large chromosomes and only a very small number of microchromosomes, the gene-rich regions are prevalently located in the few microchromosomes and in the telomeric regions of the middle-sized chromosomes (Federico et al., 2005). The distinct localization of the GC-richest and the GC-poorest bands initially observed in human chromosomes appears, therefore, to be a general feature of chromosomes from warm-blooded vertebrates. Again as in the case of mammals, the gene-richest/GC-richest chromosomal regions of chicken (and of Accipitridae) are predominantly distributed in internal locations of interphase nuclei, whereas the gene-poorest/GC-poorest DNA regions are close to the nuclear envelope (Saccone et al., 2002).

In this paper we present the first isochore map and a gene density analysis of the chicken genome. A similar analysis was recently published for fish genomes (Costantini et al., 2006, Costantini et al., in press). Together with the previously reported isochore map of the human genome (Costantini et al., 2006) the isochore map of chicken provides a new approach to the study of vertebrate evolution.