The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.

中文翻译：

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农业病原体高度抑制基因组中转座元件激活的群体基因组学


转座元件 (TE) 的活性可能是遗传多样性的重要驱动因素，TE 介导的突变具有广泛的适应性后果。为了避免 TE 活性的有害影响，一些真菌进化出了高度复杂的基因组防御，以减少 TE 在基因组中的增殖。重复诱导点突变 (RIP) 是一种真菌特异性 TE 防御机制，可有效针对重复序列。 RIP 的快速积累预计将在几代的过程中使 TE 失活。对于具有高度抑制性基因组防御的物种，TE 在种群水平上的进化动态知之甚少。在这里，我们利用高效 RIP 分析了Parastagonospora nodorum （一种小麦病原体）的 366 个全基因组序列。全球群体基因组学分析揭示了高水平的遗传多样性和频繁性重组的迹象。与对具有 RIP 的物种的预期相反，我们在多个种群中发现了近期的 TE 活动。无论人口历史如何，全球人群的 TE 组成和拷贝数几乎没有差异。微型反向重复转座子（MITE）和微型末端重复反转录转座子（TRIM）很大程度上是最近种内 TE 扩展的基础。我们推断了各个 TE 家族中的 RIP 足迹，发现最近活跃的高拷贝 TE 可能逃避了基因组防御。我们没有发现任何证据表明最近的正选择作用于 TE 介导的突变，而不是纯化选择在群体中以低插入频率维持新的 TE 插入。 我们的研究结果强调了由 TE 活性、选择和基因组抑制的联合作用建立的复杂的进化平衡。