Discovery of a large number of conserved non-coding elements (CNEs) in vertebrate genomes provides a cornerstone to elucidate molecular mechanisms of macroevolution. Extensive comparative genomics has proven that transposons such as short interspersed elements (SINEs) were an important source of CNEs. We recently characterized AmnSINE1, a SINE family in Amniota genomes, some of which are present in CNEs, and demonstrated that two AmnSINE1 loci play an important role in mammalian-specific brain development by functioning as an enhancer (Sasaki et al. Proc. Natl. Acad. Sci. USA 2008). To get more information about AmnSINE1s, we here performed a multi-species search for AmnSINE1, and revealed the distribution and evolutionary history of these SINEs in amniote genomes. The number of AmnSINE1 regions in amniotes ranged from 160 to 1200; the number in the eutherians were under 500 and the largest was that in chicken. Phylogenetic analysis established that each AmnSINE1 locus has evolved uniquely, primarily since the divergence of mammals from reptiles. These results support the notion that AmnSINE1s were amplified as an ancient retroposon in a common ancestor of Amniota and subsequently have survived for 300 Myr because of functions acquired by mutation-coupled exaptation prior mammalian radiation. On the basis of sequence homology and conserved synteny, we detected the orthologs of AmnSINE1 for candidates of further enhancer analysis, which are more conserved than two loci that were shown to have been involved in mammalian brain development. The present work provides a comprehensive data set to test the role of AmnSINE1s, many of which were exapted and contributed to mammalian macroevolution.
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