Separating derived from ancestral features of mouse and human genomes

To take full advantage of the mouse as a model organism, it is essential to distinguish lineage-specific biology from what is shared between human and mouse. Investigations into shared genetic elements common to both have been well served by the draft human and mouse genome sequences. More recently, the virtually complete euchromatic sequences of the two reference genomes have been finished. These reveal a high ( approximately 5%) level of sequence duplications that had previously been recalcitrant to sequencing and assembly. Within these duplications lie large numbers of rodent- or primate-specific genes. In the present paper, we review the sequence properties of the two genomes, dwelling most on the duplications, deletions and insertions that separate each of them from their most recent common ancestor, approx. 90 million years ago. We consider the differences in gene numbers and repertoires between the two species, and speculate on their contributions to lineage-specific biology. Loss of ancient single-copy genes are rare, as are gains of new functional genes through retrotransposition. Instead, most changes to the gene repertoire have occurred in large multicopy families. It has been proposed that numbers of such 'environmental genes' rise and fall, and their sequences change, as adaptive responses to infection and other environmental pressures, including conspecific competition. Nevertheless, many such genes may be under little or no selection.