Legrand Sylvain, Caron Thibault, Maumus Florian, Schvartzman Sol, Quadrana Leandro, Durand Eléonore, Gallina Sophie, Pauwels Maxime, Mazoyer Clément, Huyghe Lucie, Colot Vincent, Hanikenne Marc, Castric Vincent
1Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France.
2URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.
Mob DNA. 2019 Jul 17;10:30. doi: 10.1186/s13100-019-0171-6. eCollection 2019.
Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, and .
Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes.
Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.
转座元件（TEs）是基因组寄生虫，对宿主基因组结构和宿主适应性有重大影响。由于缺乏密切相关物种之间的小规模系统发育比较，对其进化意义的恰当评估受到了阻碍。在这里，我们通过比较两种密切相关的植物物种和，在微观进化尺度上表征了TE积累的动态。
对这两个异交物种的联合基因组注释证实，两者都包含两个不同的TE群体，分别具有“近期”或“古老”的插入历史。罕见分离插入的鉴定表明，不同的TE家族对这两个物种中正在进行的TE积累动态有贡献。直系同源TE片段（即那些在两个物种中都保留的片段）往往比仅在一个物种中保留的片段更靠近基因定位。与非直系同源TE插入相比，直系同源的TE插入往往产生较少的短干扰RNA，当在基因内或基因附近发现时甲基化程度较低，并且这些TE插入往往具有较低的表达水平。这些发现表明，TE插入的长期保留反映了它们频繁获得适应性作用和/或当它们靠近基因时去除近中性TE插入的有害影响。
我们的结果表明，在这两个异交物种中，TE景观具有快速的进化动态，有多种具有不同删除抗性倾向的新插入的重要输入。
