The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.
The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.
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DOI：
10.1186/s12864-016-2667-5
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发表时间：
2016-05-04
期刊：
影响因子：
4.4
通讯作者：
Vershinin AV
中科院分区：
文献类型：
--
作者：
Evtushenko EV;Levitsky VG;Elisafenko EA;Gunbin KV;Belousov AI;Šafář J;Doležel J;Vershinin AV
黑麦（黑麦）染色体的一个显着特征是存在大量亚端粒异染色质块，其大小与串联阵列的拷贝数相关。这些区域在物种形成期间形成的速度仍然无法解释。使用从黑麦染色体 1R 的短臂端体创建的 BAC 文库，我们发现了 pSc200 和 pSc250 串联重复家族的大量阵列，这些阵列集中在亚端粒异染色质中，并鉴定了相邻的 DNA 序列。阵列在单体组织中表现出显着的异质性。 454 个读数用于获得这些串联重复在整个黑麦基因组中的扩展的表示。多个相对较短的单体阵列的存在，加上单体系统发育树的主要星状拓扑，被认为是 pSc200 和 pSc250 阵列快速扩展的指示。亚端粒异染色质的进化似乎包括非法重组的重要贡献。 pSc200 和 pSc250 阵列两侧区域内转座元件 (TE) 的组成与整个基因组中的组成显着不同。 Solo-LTR 强烈富集，表明存在活跃的异位交换历史。 LTR 序列中存在过多的 DNA 基序。亚端粒异染色质的大块是由 TE 的组合活性和串联重复的扩展产生的。这种扩张很可能是基于高度复杂的重组机制网络。本文的在线版本 (doi:10.1186/s12864-016-2667-5) 包含补充材料，可供授权用户使用。
A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms. The online version of this article (doi:10.1186/s12864-016-2667-5) contains supplementary material, which is available to authorized users.