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.

中文翻译：

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全基因组转座因子的筛选和表征及其在家蚕中的分布分析。

为了阐明转座因子（TEs）对家蚕基因组结构和进化的贡献，我们使用新发布的基因组程序对TEs进行了全基因组分析。TE占基因组的35％，对基因组大小有很大贡献。非长末端重复逆转录转座子（非LTRs）和短散布的核元件（SINEs）是主要的TE类。从基因组中TE分布的特征可以看出，非LTR（尤其是R1进化枝元素）经常插入富含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积累在基因密度低的区域，TE密度与染色体重组率之间存在较强的正相关关系。我们还表征了非LTR的进化枝分布。桑蚕非LTR代表16个先前定义的进化枝中的10个，进化枝比其他基因组报道的变异最多。发现了两个部分的CRE进化枝元素，这是最古老的非LTR谱系之一，以前仅在锥虫和真菌中发现过。该分析表明，家蚕基因组受到大量数量和各种TE的影响。它是最古老的非LTR谱系之一，以前仅在锥虫和真菌中发现过。该分析表明，家蚕基因组受到大量数量和各种TE的影响。它是最古老的非LTR谱系之一，以前仅在锥虫和真菌中发现过。该分析表明，家蚕基因组受到大量数量和各种TE的影响。