Chumová Zuzana, Belyayev Alexander, Mandáková Terezie, Zeisek Vojtěch, Hodková Eva, Šemberová Kristýna, Euston-Brown Douglas, Trávníček Pavel
Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia.
Department of Botany, Faculty of Science, Charles University, Prague, Czechia.
Front Plant Sci. 2022 Sep 29;13:982852. doi: 10.3389/fpls.2022.982852. eCollection 2022.
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
非编码重复DNA（重复基因组）是核基因组的一个活跃部分，参与其结构、进化和功能。它主要由转座元件（TEs）和卫星DNA组成，并且随着时间的推移容易发生最快速的变化。TEs的活性可能导致全球基因组重组，并可能在应对环境挑战时发挥适应性或调节作用。这一假设首次应用于开普植物区系热点地区的植物，以确定重复DNA的变化是否与对恶劣但物种极其丰富的环境的反应有关。菊科植物属是一个合适的模型组，因为它在二倍体水平上显示出基因组大小的相当大的变化，并且在开普的两个主要生物群落，即菲恩博斯和肉质卡鲁，具有高且几乎相等的特有性水平。首先，我们基于多个低拷贝基因构建了一个系统发育树，作为检测重复基因组定量和定性变化的系统发育框架。其次，我们对两组TEs爆发情况不同的菊科植物的环境进行了比较分析。我们的结果表明，从肉质卡鲁到菲恩博斯的环境转变伴随着TEs爆发，这可能也推动了系统发育分歧。因此，我们假设对快速进化的重复基因组的分析可以作为确定快速辐射类群谱系分歧分子基础的重要指标。
