An exhaustive search for tandem repeats and long duplicated chromosomal regions within the mouse genome

Abstract

Traces of ancient duplications of extensive chromosomal regions are being discovered within the human genome. For example, the MHC (major histocompatibility complex) gene region on chromosome 6 (6p21.3) encodes a cluster of genes that are homologous to those on chromosome 9 (9q33-q34) . These regions appear to have arisen from regional duplication around the time of vertebrate emergence. To elucidate the evolution of mammalian genomes, it is crucial to search for duplicated chromosomal regions in the mouse genome. In this study, we searched for long duplicated chromosomal regions in the mouse genome using the map information derived from the Mouse Genome Database and the numerous homologous gene pairs from GenBank. To identify the regions, we searched for homologous gene pairs among the genomic sequences extracted from GenBank (r.118) . We defined the candidates of duplicated regions as those having more than two homologous gene pairs located within 5cM on each chromosome. We conducted a statistical test considering the distribution of homologous gene pairs and tandem repeats in the mouse genome. Twenty-seven pairs of duplicated regions were found in this study. Seven procollagen genes, three Hox gene clusters, six integrin genes, three fibroblast growth factor receptor genes and three eye absent homolog genes were located in the duplicated regions.