Impact of transposable elements on genome structure and evolution in bread wheat

First author: Thomas Wicker; Affiliations: University of Zurich (苏黎世大学): Zurich, Switzerland

Corresponding author: Frédéric Choulet

Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate (最接近的) gene vicinity (邻近) differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid. Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.

转座元件TE是大植物基因组主要的组成部分，同时也是驱动基因组演化的主要因素。最近报道的六倍体小麦揭示了高度重复序列在基因组上的分布，并提供了研究小麦三套亚染色体上重复序列动态变化的基础。尽管没有证据显示在多倍化事件之后TE发生过扩张，但小麦A、B、D三套亚染色体上平均TE含量大致相当。自从亚基因组从共同的祖先分化之后TE发生过翻天覆地的变化，但76%左右的TE家族在每个亚基因组上的比例相当。此外，尽管随着时间的推移，共线性的TE会被新的插入所替换，但是共线性基因区的间隔十分保守，说明基因之间，而非序列的分化受到演化的限制。基因附近区域的TE组成与核心基因间隔区之间的TE组成不同。作者在所有的亚基因组上基因附近区发现了相同的TE家族富集或缺失。对于长末端重复序列转座子亚家族插入时间的估计说明了在多倍化之前A、B、D三个二倍体谱系的独立演化及AB四倍体协同扩增。尽管基因间区受到了TE变化的改变，但A、B、D三个亚基因组上TE家族比例、基因间区及基因邻近TE富集等特性存在保守性。

doi: https://doi.org/10.1186/s13059-018-1479-0

Journal: Genome Biology

Published date: 17 August, 2018

（P.S. 原文下载：链接:https://pan.baidu.com/s/1qFiSsqwlF_7JjmGMbedfhQ  密码:dmu6）