Evolution of B2 repeats: the muroid explosion

B2 repeats are a group of short interspersed elements (SINEs) specific for rodent genomes. Copy numbers were determined for different rodent genera. All the Muroid (rat, mouse, deer mouse, hamster, gerbil) rodent genomes analyzed exhibited 80,000-100,000 copies per haploid genome, whereas the squirrel genome contains only 2,500 copies, and fewer than 100 (if any) copies were observed for the Hystricognath rodents (guinea pig and nutria). These findings demonstrate that there was an 'explosion' of amplification of B2 elements within muroid rodents. The similar copy number of B2 elements within the different muroid species could be explained by formation of a high proportion of the B2 elements prior to the divergence of the different muroid species. However, the 3'-end of the B2 sequence is unique between murid and cricetid rodents suggesting that the majority of elements amplified after the divergence of these species. Also consistent with recent amplification of these elements in parallel within the muroid genomes is the finding that within mouse and rat there are distinct subfamilies of B2 repeats. The pattern of consistent parallel amplification of B2 elements in muroid species contrasts with the sporadic nature of ID repeat amplification in the same genomes. The consensus of the young mouse subfamily of elements corresponds to the B2 RNA that is preferentially transcribed in embryonic, tumor, and normal liver cells. The subfamily is young based on both its low divergence from the subfamily consensus sequence and the finding that the most recent B2 element insertions in the mouse genome are members of this subfamily.