Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori
Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori
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DOI：
10.1016/j.ibmb.2008.05.012
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发表时间：
2008-12-01
影响因子：
3.8
通讯作者：
Fujiwara, Haruhiko
中科院分区：
文献类型：
--
作者：
Osanai-Futahashi, Mizuko;Suetsugu, Yoshitaka;Fujiwara, Haruhiko
为了阐明转座元件（TE）对家蚕基因组结构和进化的贡献，我们利用新发布的基因组组装对TE进行了全基因组分析。 TE 占基因组的 35%，对基因组大小贡献很大。非长末端重复反转录转座子（非 LTR）和短散布核元件（SINE）是主要的 TE 类型。从基因组中 TE 分布的特征来看，非 LTR，尤其是 R1 分支元件，经常插入到富含 GC 的区域。非LTR本身的GC含量超过40%，这表明它们对插入区GC含量的贡献。 TE在基因密度较低的区域积累，并且TE密度与染色体重组率之间存在较强的正相关性，我们还表征了非LTR的进化枝分布。家蚕非 LTR 代表了先前定义的 16 个进化枝中的 10 个，其多样性比报道的其他基因组的种类最多。发现了两个部分CRE进化枝元件，这是非LTR最古老的谱系之一，之前只在锥虫和真菌中发现过。该分析表明，家蚕基因组受到大量和多种 TE 的影响。 (C) 2008 Elsevier Ltd. 保留所有权利。
To elucidate the contribution of transposable elements (TEs) to the silkworm genome structure and evolution, we have conducted genome-wide analysis of TEs using the newly released genome assembly. The TEs made up 35% of the genome and contributed greatly to the genome size. Non-long terminal repeat retrotransposons (non-LTRs) and short interspersed nuclear elements (SINEs) were the predominant TE classes. From characterization of the TE distribution in the genome, it was revealed that non-LTRs, especially R1 clade elements, are frequently inserted into GC-rich regions. The GC content of non-LTRs themselves was over 40%, which indicate their contribution to the GC content of the insertion region. TEs accumulated in regions with low gene density, and there were relatively strong positive correlations between TE density and chromosomal recombination rate, We also characterized the clade distribution of the non-LTRs. The silkworm non-LTRs represented 10 of the 16 previously defined clades, which had the most variety than that reported for other genomes. Two partial CRE clade elements were found, which is one of the most ancient lineages of non-LTRs, and have been only found in Trypanosoma and fungi before. This analysis suggests that Bombyx genome is influenced by numerous amounts and variety of TEs. (C) 2008 Elsevier Ltd. All rights reserved.