CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown. Application of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. This approach yielded knowledge regarding: (i) the coexistence of two CACTA transposons subtypes in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv)) identification of captured satDNA arrays. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions. Our study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in the genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with the proposed novel functional features of structural-different CACTA elements can impact evolutionary trajectory of the host genome.

中文翻译：

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藜属（Amaranthaceae，Caryophyllales）物种基因组中CACTA转座子的结构多样性：特定性状及与被子植物相似元件的比较

CACTA 转座因子 (TE) 是最丰富的 2 类（剪切和粘贴）转座子超家族之一。近几十年来，CACTA 元素在植物、真菌和动物界的物种中被广泛鉴定，但仅在少数模式物种的基因组中得到充分研究，尽管非模式基因组可以带来额外和有价值的信息。它主要关注属于大型分类群基础中进化枝的物种的基因组，其基因组在一定程度上可以保存残骸和/或具有特定特征。因此，我们试图研究藜属（苋科，石竹目）物种的基因组，以揭示 CACTA 元素的结构变异性。Caryophyllales 是被子植物的一个独立分支，直到最近才知道这个进化枝中 CACTA 元素的多样性。应用短读长基因组组装算法，然后分析检测到的完整 CACTA 元件，可以确定它们在 22 种藜属植物的基因组中的结构多样性。这种方法产生了关于以下方面的知识：（i）两个 CACTA 转座子亚型在单个基因组中的共存；(ii) 在编码序列中获得额外的蛋白质保守结构域；(iii) 是否存在捕获的基因片段，包括花卉发育的关键基因；(iv)) 识别捕获的 satDNA 阵列。广泛的比较数据库分析表明，已识别的事件以不同的比例分散在被子植物中。我们的研究表明，在保留基本元素结构的同时，CACTA 转座子的广泛编码和非编码添加发生在 C. album 聚合物种的基因组中。重新定位基因组内添加物的能力与结构不同的 CACTA 元件的新功能特征相结合，可以影响宿主基因组的进化轨迹。