Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster.
Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster.
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DOI：
10.1093/gbe/evx050
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发表时间：
2017-05-01
影响因子：
3.3
通讯作者：
Schaack S
中科院分区：
文献类型：
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作者：
Adrion JR;Song MJ;Schrider DR;Hahn MW;Schaack S
了解转座因子（TE）插入和删除的速率对于理解它们在基因组进化中的作用至关重要。我们估计所有已知的，活跃的TE超家族的插入和删除的自发率存在于一组果蝇突变积累（MA）线使用全基因组序列数据。我们的研究结果表明，TE插入远远超过TE缺失D。黑腹菌我们发现背景基因型对TE活性有显著影响，在一个MA系中插入率较高。我们还发现染色体之间的显着率异质性，与插入和缺失率升高的X相对于常染色体。此外，我们确定了显着的TE活动和染色质状态之间的关联，并测试TE活动和其他功能的本地基因组环境，如TE含量，外显子含量，GC含量和重组率之间的关联。我们的研究结果提供了迄今为止任何生物体中TE流动性的最详细评估，并为解决TE动力学的理论预测和探索D中TE运动的大规模模式提供了有用的基准。Melanogaster和其他物种。
Knowing the rate at which transposable elements (TEs) insert and delete is critical for understanding their role in genome evolution. We estimated spontaneous rates of insertion and deletion for all known, active TE superfamilies present in a set of Drosophila melanogaster mutation-accumulation (MA) lines using whole genome sequence data. Our results demonstrate that TE insertions far outpace TE deletions in D. melanogaster. We found a significant effect of background genotype on TE activity, with higher rates of insertions in one MA line. We also found significant rate heterogeneity between the chromosomes, with both insertion and deletion rates elevated on the X relative to the autosomes. Further, we identified significant associations between TE activity and chromatin state, and tested for associations between TE activity and other features of the local genomic environment such as TE content, exon content, GC content, and recombination rate. Our results provide the most detailed assessment of TE mobility in any organism to date, and provide a useful benchmark for both addressing theoretical predictions of TE dynamics and for exploring large-scale patterns of TE movement in D. melanogaster and other species.