Molecular Biology and Evolution, Vol 11, 886-898, Copyright © 1994 by Society for Molecular Biology and Evolution
TL Vandergon and M Reitman
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.
ORIGINAL ARTICLE
Evolution of chicken repeat 1 (CR1) elements: evidence for ancient subfamilies and multiple progenitors
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-1770.
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