A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 50–80 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass.

长末端重复序列反转录转座子（LTR retrotransposons）通常是植物基因组中丰度最高的组成成分，可对基因及基因组进化产生重要影响。目前已报道的LTR反转录转座子多为长度大于4 kb的大型元件，且大多分布于异染色质（基因贫乏）区域。本研究报道了迄今发现的最小LTR反转录转座子，其长度仅为292 bp。该元件存在于水稻、玉米、高粱及其他禾本科物种的基因组中，表明其至少在5000万至8000万年前就已存在于禾本科物种的祖先基因组中。通过插入时间估算、不同已测序水稻品系间的比较分析以及信使RNA（mRNA）数据的研究结果显示，该元件在部分基因组中仍可能具有活性。与其他LTR反转录转座子不同，这类小型LTR反转录转座子（SMARTs）广泛分布于全基因组中，且常位于基因内部或基因附近，其插入模式与微型反向重复转座元件（miniature inverted repeat transposable elements，MITEs）高度相似。本研究数据表明，SMARTs插入基因内部或基因附近时，在少数案例中可同时改变基因结构与基因表达。为进一步验证其在基因表达调控中的作用，本研究还鉴定到了SMARTs特异性小RNA（sRNAs），这类小RNA可能参与基因调控过程。因此，SMARTs可能在基因组进化及基因创新中发挥了重要作用，同时也可为禾本科物种的基因标记系统提供极具价值的工具。