Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time.

中文翻译：

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牛肝菌基因组揭示了转座子的多种影响。

小麦是一种重要的全球农作物，其基因组非常庞大且复杂，与其他任何已知农作物物种相比，其转座因子（TEs）含量更高。在这里，我们生成了小麦D基因组的供体Aegilops tauschii的染色体级高质量参考基因组，其中92.5％的序列已锚定在染色体上。使用此程序集，我们准确地表征了基因位点，基因表达，假基因，甲基化，重组率，microRNA，尤其是染色体上的TE。除了发现一波最近的基因复制浪潮之外，我们还检测到TEs出现在大约一半的基因中，并且发现这些基因的表达水平低于没有TEs的基因，这可能是由于它们的甲基化水平升高所致。我们绘制了所有小麦分子标记，并构建了与基因组序列相对应的高分辨率整合遗传图谱，从而将先前检测到的农学上重要的基因/定量性状基因座（QTL）放在了Ae上。tauschii基因组首次出现。