Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the Mediterranean grass Brachypodium distachyon

Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. ...

转座因子（Transposable element, TE）的活性现已成为导致物种间基因组大小与结构变异的主要成因之一。然而，转座因子对物种内遗传变异与分化的贡献程度仍远未明晰，这主要是因为迄今为止群体基因组学数据仅在经典模式生物中可获取。本研究以一年生地中海草本植物二穗短柄草（Brachypodium distachyon）为研究对象，探究其自然种群中的转座因子动态。研究人员利用53份自然种质的全基因组测序数据，在受试基因组中鉴定出超过5400个转座因子多态性位点。研究首先发现：尽管种群瓶颈与扩张事件塑造了二穗短柄草的遗传多样性，但此类事件并未如其他物种中所观测到的那样，引发转座因子家族的谱系特异性激活。与之相反，同一转座因子家族在该物种的整个分布范围内均保持活跃，且转座因子活性在不同种群间呈现均一分布特征，这表明存在保守的调控机制……