PMID:9582191

Citation	Kim, JM, Vanguri, S, Boeke, JD, Gabriel, A and Voytas, DF (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464-78
Abstract	We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs and the identification of a distinct Ty1 subfamily (Ty1'). Whereas Ty1, Ty2, and Ty5 LTRs displayed a broad range of sequence diversity (typically ranging from 70%-99% identity), Ty3 and Ty4 LTRs were highly similar within each element family (most sharing >96% nucleotide identity). Therefore, Ty3 and Ty4 may be more recent additions to the S. cerevisiae genome and perhaps 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 bases of tRNA genes or other genes transcribed by RNA polymerase III. tRNA 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'-flanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons can influence genome organization. S. cerevisiae offers the first opportunity to view organizational and evolutionary trends among retrotransposons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to other, more complex genomes.
Links	PubMed
Keywords	Base Sequence; Chromosome Mapping; Chromosomes, Fungal/genetics; Consensus Sequence/genetics; DNA, Fungal/analysis; Gene Rearrangement; Genome, Fungal; Multigene Family; Reading Frames/genetics; Retroelements/genetics; Saccharomyces cerevisiae/genetics; Sequence Analysis, DNA
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
YEAST:YD11B	involved_in	GO:0032197: transposition, RNA-mediated	ECO:0000250: sequence similarity evidence used in manual assertion		P		Seeded From UniProt	Missing: with/from
YEAST:YD11B	enables	GO:0008233: peptidase activity	ECO:0000250: sequence similarity evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from
YEAST:YD11B	enables	GO:0004540: ribonuclease activity	ECO:0000250: sequence similarity evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from
YEAST:YD11B	enables	GO:0003964: RNA-directed DNA polymerase activity	ECO:0000250: sequence similarity evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from
YEAST:YD11B	enables	GO:0003887: DNA-directed DNA polymerase activity	ECO:0000250: sequence similarity evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from
YEAST:YD11B	enables	GO:0003723: RNA binding	ECO:0000250: sequence similarity evidence used in manual assertion		F		Seeded From UniProt	Missing: with/from
YEAST:YD11B	part_of	GO:0000943: retrotransposon nucleocapsid	ECO:0000250: sequence similarity evidence used in manual assertion		C		Seeded From UniProt	Missing: with/from

References

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