Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions
Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions
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DOI：
10.1007/s10577-018-9579-y
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发表时间：
2018-05
影响因子：
2.6
通讯作者：
Kenta Nakashima;J. Abe;A. Kanazawa
中科院分区：
文献类型：
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作者：
Kenta Nakashima;J. Abe;A. Kanazawa
逆转录转座子构成植物基因组的很大一部分。已经使用几种植物的基因组测序数据分析了多种反转录转座子的染色体分布，但转座的进化谱已经表征了有限数量的反转录转座子家族。在这里，我们利用基因组测序数据表征了大豆反转录转座子 SORE-1 家族的 96 个元件。每个 SORE-1 元件插入基因组的时间是根据 5' 和 3' 长末端重复序列 (LTR) 之间的序列差异来估计的。将此估计与这些元件的染色体位置信息相结合，我们发现现有的 SORE-1 插入基因丰富的染色体臂平均比插入基因贫乏的着丝粒周围区域更晚。此外，100万年前之后，染色体臂的插入数量和插入比例都大幅增加。在这些区域中以相似的频率检测到单独的 LTR，这表明通过不等同源重组消除 SORE-1 是公正的。总而言之，这些结果表明最近将 SORE-1 插入到包含常染色质区域的染色体臂中的倾向。这一观点与早期从大豆反转录转座子整体分析中推导出来的观点相反，并表明不同反转录转座子家族之间的染色体分布模式可能比之前认为的更加多样化。
Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of theSORE-1family of soybean retrotransposons using genome sequencing data. Insertion time of eachSORE-1element into the genome was estimated on the basis of sequence differences between the 5′ and 3′ long terminal repeats (LTRs). Combining this estimation with information on the chromosomal location of these elements, we found that the insertion of the existingSORE-1into gene-rich chromosome arms occurred on average more recently than that into gene-poor pericentromeric regions. In addition, both the number of insertions and the proportion of insertions into chromosome arms profoundly increased after 1 million years ago. Solo LTRs were detected in these regions at a similar frequency, suggesting that elimination ofSORE-1via unequal homologous recombination was unbiased. Taken together, these results suggest the preference of a recent insertion ofSORE-1into chromosome arms comprising euchromatic regions. This notion is contrary to an earlier view deduced from an overall profiling of soybean retrotransposons and suggests that the pattern of chromosomal distribution can be more diverse than previously thought between different families of retrotransposons.