Evolution of chicken repeat 1 (CR1) elements: evidence for ancient subfamilies and multiple progenitors

Chicken repeat 1 (CR1) is an interspersed repetitive element that is a member of the non-long terminal repeat class of retrotransposons. A data set of chicken 95 CR1 elements was compiled and the phylogeny of the 52 elements with the most complete 3' ends was examined. We interpret the branching pattern as clustering into at least six subfamilies, designated A-F. The presence of highly similar elements within the B, C, D, and F subfamilies is evidence that a distinct progenitor has spawned each of these subfamilies. The nucleotide divergence between members of subfamily C was 5%-8%, suggesting that this subfamily has undergone a relatively recent burst of retrotransposition. The A and E subfamilies may have been spawned from ancestors of these four progenitors or from other, distinct progenitors. The consensus sequences for the six subfamilies showed considerable divergence, implying that the CR1 subfamilies are ancient. The CR1 elements in each subfamily have truncated 5' ends and a 3' end consisting of > or = 2 repeats of an 8-bp sequence. We estimate that there are approximately 100,000 CR1 elements in the chicken genome. Twelve CR1 sequences from avian species other than chicken were identified. Some of these sequences grouped into different subfamilies, demonstrating that multiple subfamilies existed early in avian evolution. Reptilian CR1 sequences were also identified, demonstrating that the CR1 element arose before the divergence of birds and reptiles.