Juretic Nikoleta, Hoen Douglas R, Huynh Michael L, Harrison Paul M, Bureau Thomas E
Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada.
Genome Res. 2005 Sep;15(9):1292-7. doi: 10.1101/gr.4064205.
DNA transposons are known to frequently capture duplicated fragments of host genes. The evolutionary impact of this phenomenon depends on how frequently the fragments retain protein-coding function as opposed to becoming pseudogenes. Gene fragment duplication by Mutator-like elements (MULEs) has previously been documented in maize, Arabidopsis, and rice. Here we present a rigorous genome-wide analysis of MULEs in the model plant Oryza sativa (domesticated rice). We identify 8274 MULEs with intact termini and target-site duplications (TSDs) and show that 1337 of them contain duplicated host gene fragments. Through a detailed examination of the 5% of duplicated gene fragments that are transcribed, we demonstrate that virtually all cases contain pseudogenic features such as fragmented conserved protein domains, frameshifts, and premature stop codons. In addition, we show that the distribution of the ratio of nonsynonymous to synonymous amino acid substitution rates for the duplications agrees with the expected distribution for pseudogenes. We conclude that MULE-mediated host gene duplication results in the formation of pseudogenes, not novel functional protein-coding genes; however, the transcribed duplications possess characteristics consistent with a potential role in the regulation of host gene expression.
已知DNA转座子经常捕获宿主基因的重复片段。这一现象的进化影响取决于这些片段保留蛋白质编码功能的频率，而非成为假基因的频率。此前已在玉米、拟南芥和水稻中记录了类Mutator元件（MULE）导致的基因片段重复。在此，我们对模式植物水稻（栽培稻）中的MULE进行了严格的全基因组分析。我们鉴定出8274个具有完整末端和靶位点重复（TSD）的MULE，并表明其中1337个含有重复的宿主基因片段。通过对转录的重复基因片段中的5%进行详细检查，我们证明几乎所有情况都含有假基因特征，如片段化的保守蛋白质结构域、移码突变和过早的终止密码子。此外，我们表明重复序列中非同义氨基酸替换率与同义氨基酸替换率的比值分布与假基因的预期分布一致。我们得出结论，MULE介导的宿主基因重复导致假基因的形成，而非新的功能性蛋白质编码基因；然而，转录的重复序列具有与宿主基因表达调控潜在作用相一致的特征。
