The pig genome: compositional analysis and identification of the gene-richest regions in chromosomes and nuclei

Abstract

The isochore organization of the mammalian genome comprises a general pattern and some special patterns, the former being characterized by a wider compositional distribution of the DNA fragments. The large majority of the mammalian genomes belong to the former, and only some groups, such as the Myomorpha sub-order of Rodentia, belong to the latter. Here we describe the compositional organization of the pig ( Sus scrofa) genome that belongs to the general mammalian pattern. We investigated (i) the compositional distribution of the genes by analysis of their GC 3 levels (the GC levels at the third codon positions), and (ii) the correlation between the GC 3 value of orthologous genes from pig and other vertebrates (human, calf, mouse, chicken, and Xenopus). As expected, the highest gene concentration corresponded to the H3 isochore family, and the highest GC 3 correlations were observed in the pig/human and pig/calf comparisons. Then we identified, by in situ hybridization of the GC-richest H3 isochores, the pig chromosomal regions endowed by the highest gene-density that largely corresponded to the telomeric chromosomal bands. Moreover, we observed that these gene-rich bands are syntenic with the previously identified GC-richest/gene richest H3+ bands of the human chromosomes. At the cell nucleus level, we observed that the gene-dense region corresponded to the more internal compartment, as previously found in human and avian cell nuclei.