Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives. Stowaway MITEs are derived from and mobilised by elements from the mariner superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by Daucus carota Stowaway MITEs (DcStos), their association with genes and their putative impact on genome evolution has not been comprehensively analysed. Fourteen families of Stowaway elements DcStos occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated Daucus carota, yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism. DcSto element demography differed based on the origin of the host populations, and corresponded with the four major groups of D. carota, wild European, wild Asian, eastern cultivated and western cultivated. The DcStos elements were associated with genes, and most frequently occurred in 5′ and 3′ untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly, DcSto copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all DcSto insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The DcSto7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified Dcmar1 as an active carrot mariner element and a possible source of the transposition machinery for DcSto7b. Stowaway MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

中文翻译：

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偷渡的微型反向重复转座因子是推动近期野生和栽培胡萝卜基因组多样性的重要因素

微型反向重复转座元件 (MITE) 是小型非自主 DNA 转座子，在植物基因组中普遍存在，并由其自主亲属动员。Stowaway MITEs 来源于水手超家族的元素并由它们动员。这些元素构成了胡萝卜基因组的重要组成部分；然而，由胡萝卜偷渡螨（DcStos）引起的变异、它们与基因的关联以及它们对基因组进化的推定影响尚未得到全面分析。十四个偷渡元素家族 DcStos 约占胡萝卜基因组的 0.5%。我们系统分析了 31 个野生和栽培胡萝卜基因组，产生了 1.85 万份这些元素，显示出显着的插入位点多态性。DcSto元素人口学因寄主种群的来源而异，与D. carota、欧洲野生、亚洲野生、东方栽培和西方栽培四大类群相对应。DcStos 元件与基因相关，最常见于 5' 和 3' 非翻译区 (UTR)。各个家庭在特定基因片段中存在的倾向不同。最重要的是，基因上游和下游 2 kb 区域中的 DcSto 拷贝更频繁地与编码转录因子的开放阅读框相关，表明它们可能对功能产生影响。不同宿主基因组中超过 1.5% 的 DcSto 插入位点在完全相同的位置包含不同的拷贝，表明存在插入热点。DcSto7b 家族比栽培胡萝卜中的其他家族更具多态性。一系列证据表明它在胡萝卜驯化过程中的活动，并确定 Dcmar1 是一个活跃的胡萝卜水手元素，也是 DcSto7b 转座机制的可能来源。Stowaway MITE 对胡萝卜基因组的结构和功能变异性做出了重大贡献。