Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.
Abundance and distribution of transposable elements in two Drosophila QTL mapping resources.
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DOI：
10.1093/molbev/mst129
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发表时间：
2013-10
影响因子：
10.7
通讯作者：
Thornton KR
中科院分区：
文献类型：
--
作者：
Cridland JM;Macdonald SJ;Long AD;Thornton KR
在这里，我们提出了计算机器，以有效和准确地确定转座因子（TE）插入146个下一代测序的近交系果蝇。我们在研究中使用的品系组由来自一对遗传图谱资源的品系组成：果蝇遗传参考组（DGRP）和果蝇合成种群资源（DSPR）。我们在这些品系中鉴定了23，087个TE插入，其中83.3%仅在一个品系中发现。基因组中的元件分布有明显的差异，在X染色体上发现的TE密度较高，并且在低重组区域。如果TE位于常染色体基因组中的随机位置，我们还确定了比预期的更多的内含子序列的每个碱基对的TE和更少的外显子序列的每个碱基对的TE。基因间的TE负荷存在显著差异。例如，出轨和出轨-2旁系同源物在TE插入的数量上显示出显著差异，这可能反映了作用于这些基因座的选择的差异。当考虑TE家族时，我们发现基因家族大小对每个基因的TE插入的影响非常弱，这表明随着基因家族大小的增加，该家族内给定基因中的TE插入的数量也增加。已知TE与某些表型相关，我们的数据将允许研究人员使用DGRP和DSPR更普遍地评估TE插入在复杂性状变异中的功能作用。值得注意的是，由于大多数TE非常罕见并且通常仅限于单个品系，导致个体间表型差异的致病性TE通常可能无法在作图组中复制，因为单个元件不太可能在两个组中分离。我们的数据表明，“负担测试”，测试作为一个类的TE的效果可能更富有成效。
Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful.
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影响因子：
4.5
作者：
Hahn MW;Han MV;Han SG
通讯作者：
Han SG
DOI：
10.1073/pnas.0702552104
发表时间：
2007-07-03
影响因子：
11.1
作者：
Bergman, Casey M.;Bensasson, Douda
通讯作者：
Bensasson, Douda
影响因子：
64.8
作者：
Chanock, Stephen J.;Manolio, Teri;Collins, Francis S.
通讯作者：
Collins, Francis S.
影响因子：
64.8
作者：
Biemont, Christian;Vieira, Cristina
通讯作者：
Vieira, Cristina
影响因子：
3.3
作者：
Chung, Henry;Bogwitz, Michael R.;Daborn, Phillip J.
通讯作者：
Daborn, Phillip J.