Institute of Botany, Technische Universität Dresden, Dresden, Germany.
Ann Bot. 2021 Jan 1;127(1):91-109. doi: 10.1093/aob/mcaa176.
Plant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.
We identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.
All 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes - mechanisms that likely caused Cassandra's subfamily formation and diversification.
We traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.
植物基因组包含许多逆转录转座子及其衍生物，它们的序列快速更替。由于非自主逆转录转座子不编码任何蛋白质，它们受到的选择压力较小，导致它们多样化成多个家族，通常局限于少数几个密切相关的物种。相比之下，微型（TRIMs）非编码 Cassandra 末端重复逆转录转座子在许多植物中广泛存在。它们的标志是长末端重复（LTR）中保守的 5S rDNA 衍生启动子。由于甜菜（Beta vulgaris）具有描述良好的 LTR 逆转录转座子景观，我们旨在研究甜菜和相关基因组中的 TRIMs。
我们在甜菜参考基因组中鉴定了 Cassandra 逆转录转座子，并对其结构关系进行了描述。通过 Southern 和荧光原位杂交验证了 Cassandra-TRIMs 在苋科基因组中的基因组织、染色体定位和分布。
甜菜基因组中的 638 个 Cassandra 序列都含有保守的 LTR，因此构成了一个单一的家族。然而，可变的内部区域需要在 B. vulgaris 内分为两个 Cassandra 亚家族。相关的藜科作物 quinoa 含有第三个亚家族。这些亚家族在苋科基因组中的分布、插入时间和小 RNA 沉默程度上有所不同。Cassandra 逆转录转座子产生了许多结构变体，如单 LTR 或串联排列的 Cassandra 逆转录转座子。这些 Cassandra 衍生物表明模板转换和重组过程之间存在相互作用，这些机制可能导致了 Cassandra 的亚家族形成和多样化。
我们追踪了 Amaranthaceae 中 Cassandra 的进化，并在短的内部区域内检测到相当大的变异性，而 LTR 在序列和长度上都保持着强烈的保守性。这些特征可能使 Cassandra 成为不等交换重组的主要目标，从而导致了观察到的结构多样性，这是 LTR 介导的进化机制对宿主基因组影响的一个例子。
