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首页> 外文OA文献 >Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms
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Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

机译：Tribolium castaneum基因组中串联重复序列的全基因组分析显示，常染色体染色体臂中具有卫星DNA特征的丰富且高度动态的串联重复序列家族

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摘要

Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic chromosomal arms and clear predominance of satellite DNA-typical 170 bp monomers in arrays of ≥5 repeats. By applying different experimental approaches, we revealed that the nine most prominent TR families Cast1–Cast9 extracted from the assembly comprise ∼4.3% of the entire genome and reside almost exclusively in euchromatic regions. Among them, seven families that build ∼3.9% of the genome are based on ∼170 and ∼340 bp long monomers. Results of phylogenetic analyses of 2500 monomers originating from these families show high-sequence dynamics, evident by extensive exchanges between arrays on non-homologous chromosomes. In addition, our analysis shows that concerted evolution acts more efficiently on longer than on shorter arrays. Efficient genome-wide distribution of nine TR families implies the role of transposition only in expansion of the most dispersed family, and involvement of other mechanisms is anticipated. Despite similarities in sequence features, FISH experiments indicate high-level compartmentalization of centromeric and euchromatic tandem repeats.
机译：尽管卫星DNA是异染色质和着丝粒的良好探索成分，但对结构相对应的串联重复序列（TRs）的出现，扩散和可能对全基因组范围的影响知之甚少。我们对组装的Tribolium castaneum基因组进行的生物信息学分析表明，常染色体染色体臂中TR的重要贡献以及≥5个重复序列的卫星DNA典型170 bp单体的明显优势。通过应用不同的实验方法，我们揭示了从装配中提取的9个最著名的TR家族Cast1-Cast9占整个基因组的约4.3％，并且几乎仅位于常染色体区域。其中，七个构成基因组约3.9％的家族基于约170和340 bp长的单体。对来自这些家族的2500个单体进行系统发育分析的结果显示出高序列动力学，这在非同源染色体上的阵列之间进行了广泛的交换就很明显。此外，我们的分析表明，协同进化对更长的阵列比对较短的阵列更有效。九个TR家族的有效全基因组分布意味着转座仅在最分散家族的扩展中发挥作用，并且预计会涉及其他机制。尽管序列特征相似，但FISH实验仍表明着丝粒和常色串联重复序列具有较高的区室性。

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