Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

多倍体化和转座因子（TE）活性都是植物基因组进化的主要驱动力。在这里，我们利用Zea-Tripsacum进化枝研究共享多倍体化事件后的TE活性和积累。比较除了两个紧密相关的二倍体物种U.lydigitum digitatum和Sorghum bicolor外，各种Zea和Trispacum物种的TE进化动力学，还揭示了该研究中所有类群的重复含量变化。与高粱相比，Urelytrum的重复组成与Zea和Tripsacum的重复组成更相似尽管基因组大小与后者相似。尽管LTR-逆转录转座子在所有物种中都丰富，但我们观察到了Copia超家族的扩展，特别是在适应更温带环境的玉米（Z. mays）和T. dactyloides中。这些反转录元素的基因组分布的其他分析提供了证据，证明在接近包括植物发育，防御和大分子生物合成在内的各种生物过程的基因附近有偏向的插入。具体来说，在非生物胁迫反应涉及的基因附近，玉米和拟南芥中的盲肠插入显着富集，表明后期进化独立玉米-Tripsacum发散。双色链球菌的直系同源基因附近缺乏盲区插入提示多倍体化过程中产生的重复基因拷贝可能为TEs插入提供了新的中性位点，从而为通过TE插入诱变进行亚功能化提供了途径。