Data from: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive Cottus”, n=11) and its parental species Cottus rhenanus (n=17) and Cottus perifretum (n=9) using a reference genome assembled from long single molecule PacBio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10 – 197 %). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase of novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genome-wide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed over-abundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected.杂交作用可诱导转座子（transposons）跳跃至新的基因组位置，进而可能导致其在全基因组范围内累积。此外，转座子拷贝数也可通过基因组高度重复区域内的非等位（异位）同源重组得以扩增。目前，转座子爆发增殖与基于重组的机制在演化过程中的相对贡献仍不明确，原因是针对自然系统中转座子动态变化的研究较为匮乏。我们依托单分子PacBio长读长测序组装的参考基因组，对一个年轻杂交谱系（"侵袭性杜父鱼"，样本量n=11）及其亲本物种莱茵杜父鱼（Cottus rhenanus，n=17）和佩氏杜父鱼（Cottus perifretum，n=9）中的转座子插入全基因组分布特征进行了评估。同时，从同一批测序数据中重构转座因子（transposable elements）的完整名录并完成注释。本研究涉及的757个转座子中，有120个（占比15.9%）在该杂交谱系内的拷贝数出现上升，平均增幅达69%（区间：10%~197%）。结合该杂交谱系的形成时间来看，这表明其自杂交起始以来，仅经历数百代便完成了转座子的快速增殖。不过，转座子插入的频率谱分析显示，基因组已组装区域内的新型稀有插入事件并未出现增加。这意味着转座子更多地整合到了当前仍难以组装的基因组重复区域中。未来的研究需进一步验证：基于重组的机制是否比全基因组转座更能解释该杂交谱系中近期出现的多数转座子增殖现象。无论背后的具体机制为何，本次研究观察到的转座子在基因组重复区域的过度富集现象，均提示基因富集区域不太可能受到直接影响。