TRANSPOSABLE ELEMENTS AND GENOME ORGANIZATION - A COMPREHENSIVE SURVEY OF RETROTRANSPOSONS REVEALED BY THE COMPLETE SACCHAROMYCES-CEREVISIAE GENOME SEQUENCE

We conducted a genome-wide survey of Saccharomyces cerevisiae retrotra nsposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-Five pet cent of in sertions were solo long terminal repeats (LTRs) or LTR fragments. Over all, retrotransposon sequences constitute >377 kb or 3.1% of the genom e. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that dist inguishes the highly similar Ty1 and Ty2 LTRs and the identification o f a distinct Ty1 subfamily (Ty1'). Whereas Ty1, Ty2, and Ty5 LTRs disp layed a broad range of sequence diversity (typically ranging from 70%- 99% identity), Ty3 and Ty4 LTRs were highly similar within each elemen t family (most sharing >96% nucleotide identity). Therefore, Ty3 and T y4 may be more recent additions to the S. cerevisiae genome and perhap s entered through horizontal transfer or past polyploidization events. Distribution of Ty elements is distinctly nonrandom: 90% of Ty1, 82% of Ty2, 95% of Ty3, and 88% of Ty4 insertions were found within 750 ba ses of tRNA genes or other genes transcribed by RNA polymerase III. tR NA genes are the principle determinant of retrotransposon distribution , and there is, on average, 1.2 insertions per tRNA gene. Evidence for recombination was found near many Ty elements, particularly those not associated with tRNA gene targets. For these insertions, 5'- and 3'-f lanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons ca n influence genome organization. S. cerevisiae offers the first opport unity to view organizational and evolutionary trends among retrotransp osons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to othe r, more complex genomes.