Transposable element diversity remains high in gigantic genomes
Transposable element diversity remains high in gigantic genomes
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DOI：
10.1007/s00239-022-10063-3
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发表时间：
2021-08
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影响因子：
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通讯作者：
Ava Louise Haley;R. Mueller
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文献类型：
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作者：
Ava Louise Haley;R. Mueller
转座元件 (TE) 是在整个基因组中复制和增殖的 DNA 重复序列。总而言之，基因组中的所有 TE 形成了多样化的序列群落，可以对其进行研究以得出有关基因组进化的结论。 TE 多样性可以使用考虑物种丰富度和均匀度的生态群落多样性模型来测量。一些模型预测，随着基因组的扩展，由于异位重组的选择和/或 TE 之间的竞争以获得宿主复制机制并逃避宿主沉默机制，TE 多样性会减少。蝾螈拥有最大的脊椎动物基因组和最高的 TE 负载。尤其是无蝾螈属的蝾螈，其基因组大小从 20 到 70 Gb 不等。在这里，我们使用牛津纳米孔测序来生成四种无齿象的低覆盖率基因组序列，其中包括两个独立的基因组扩展事件，一种位于东部分支（Plethodon cinereus，29.3 Gb vs.Plethodon gluinosus，38.9 Gb），一种位于西部分支（Plethodon vehiculum，46.4 Gb vs Plethodon idahoensis， 67.0 GB）。我们对这些基因组中的TE进行了分类，发现了>40个TE超家族，占基因组的22-27%。我们计算了 Simpson 和 Shannon 多样性指数来量化总体 TE 多样性。在两次成对比较中，较小和较大基因组的多样性指数值几乎相同。这一结果表明，当基因组达到极大尺寸时，它们在超家族水平上保持高水平的 TE 多样性，这与之前对较小基因组的研究所做的预测相反。
Transposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genusPlethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species ofPlethodonthat encompass two independent genome expansion events, one in the eastern clade (Plethodon cinereus,29.3 Gb vs.Plethodon glutinosus,38.9 Gb) and one in the western clade (Plethodon vehiculum,46.4 Gb vsPlethodon idahoensis, 67.0 Gb). We classified the TEs in these genomes and found > 40 TE superfamilies, accounting for 22–27% of the genomes. We calculated Simpson’s and Shannon’s diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.