Transposable elements and genome organization:: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence
Transposable elements and genome organization:: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence
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DOI：
10.1101/gr.8.5.464
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发表时间：
1998-05-01
期刊：
影响因子：
7
通讯作者：
Voytas, DF
中科院分区：
文献类型：
--
作者：
Kim, JM;Vanguri, S;Voytas, DF
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个插入片段，包括217个Ty1、34个Ty2、41个Ty3、32个Ty4和7个Ty5。85%的插入片段是单长末端重复序列(LTRs)或LtR片段。总体而言，反转录转座子序列构成了377kb或3.1%的基因组。反转录转座子序列的独立进化通过鉴定区分高度相似的Ty1和TY2 LTrs的单碱基对插入/缺失和鉴定出不同的Ty1亚家族(Ty1‘)来证明。虽然Ty1、TY2和TY5 LTrs显示出广泛的序列多样性(通常在70%-99%的同源性范围内)，但Ty3和Ty4 LTrs在每个元素家族中高度相似(大多数共享96%的核苷酸同源性)。因此，Ty3和Ty4可能是酿酒酵母基因组中较新的成员，可能是通过水平转移或过去的多倍化事件进入的。TY元件的分布具有明显的非随机性：90%的Ty1、82%的TY2、95%的Ty3和88%的Ty4插入片段位于由RNA聚合酶III转录的tRNA基因或其他基因的750个碱基内。tRNA基因是逆转录转座子分布的主要决定因素，平均每个tRNA基因有1.2个插入片段。在许多Ty元件附近发现了重组的证据，特别是那些与tRNA基因靶标无关的元件。在这些插入中，5‘和3’侧翼序列经常在多条染色体之间复制和重排，这表明反转录转座子之间的重组可以影响基因组的组织。酿酒酵母首次提供了在基因组水平上观察反转录转座子之间的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和与其他更复杂的基因组进行比较的起点。
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 pet cent 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.