Kim J M, Vanguri S, Boeke J D, Gabriel A, Voytas D F
Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA.
Genome Res. 1998 May;8(5):464-78. doi: 10.1101/gr.8.5.464.
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.
我们对酿酒酵母反转录转座子进行了全基因组调查，共鉴定出331个插入序列，其中包括217个Ty1、34个Ty2、41个Ty3、32个Ty4和7个Ty5元件。85%的插入序列为单独的长末端重复序列（LTR）或LTR片段。总体而言，反转录转座子序列构成了超过377 kb或基因组的3.1%。反转录转座子序列的独立进化通过以下证据得以证明：鉴定出一个单碱基对插入/缺失，该插入/缺失区分了高度相似的Ty1和Ty2 LTR，以及鉴定出一个独特的Ty1亚家族（Ty1'）。虽然Ty1、Ty2和Ty5 LTR表现出广泛的序列多样性（通常同一性范围为70%-99%），但Ty3和Ty4 LTR在每个元件家族内高度相似（大多数共享>96%的核苷酸同一性）。因此，Ty3和Ty4可能是酿酒酵母基因组中较新的添加物，可能是通过水平转移或过去的多倍体化事件进入的。Ty元件的分布明显是非随机的：90%的Ty1、82%的Ty2、95%的Ty3和88%的Ty4插入序列位于tRNA基因或其他由RNA聚合酶III转录的基因的750个碱基内。tRNA基因是反转录转座子分布的主要决定因素，平均每个tRNA基因有1.2个插入序列。在许多Ty元件附近发现了重组证据，特别是那些与tRNA基因靶点无关的元件。对于这些插入序列，5'和3'侧翼序列经常在多条染色体之间重复和重排，表明反转录转座子之间的重组可以影响基因组组织。酿酒酵母提供了第一个在基因组水平上观察反转录转座子组织和进化趋势的机会，我们希望我们汇编的数据将作为进一步研究以及与其他更复杂基因组进行比较的起点。
