Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.
Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.
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DOI：
10.1186/1471-2164-7-269
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发表时间：
2006-10-23
期刊：
影响因子：
4.4
通讯作者：
Bosch M
中科院分区：
文献类型：
--
作者：
López-Giráldez F;Andrés O;Domingo-Roura X;Bosch M
由于微型卫星的许多应用，其普及程度在过去十年中大大提高。然而，目前很少有人了解的因素，影响其发生和分布之间和物种基因组内。本研究利用GenBank中的食肉动物微卫星克隆，分析了它们与散置重复序列的关联，并阐明了散置重复序列在微卫星发生和分布中的作用。我们构建了一个全面的食肉动物微卫星数据库，包括1236个克隆从GenBank中。代表了12个食肉动物家庭中的11个33种，尽管两个远亲物种，家犬和猫，显然是过度代表。在这些克隆中，330个含有tRNALys衍生的西内斯，357个含有其他散布的重复序列。我们对每个单倍体基因组的tRNA SINE拷贝数的粗略估计比已发表的要高得多。我们的研究结果还揭示了AG和A-丰富的重复序列和tRNALys衍生的西内斯的明显并列，表明它们的共同进化。这两个微卫星重复出现在两个区域的insterspersed重复。此外，与tRNALys衍生的西内斯相关的微卫星显示出最高的复杂性和较小的潜在不稳定性。我们的研究结果表明，tRNALys衍生的西内斯是食肉动物微卫星产生的重要来源，特别是对于AG和富含A的重复基序。这些观察结果表明两种模式的微卫星生成：扩展和变化的预先存在的串联重复序列和转换的序列具有高的神秘的简单性到一个重复阵列，机制是不是特定的tRNALys衍生的西内斯。微卫星和散布重复序列的协同进化也可以解释重复序列在物种间和物种内的不同分布。最后，由于其较高的复杂性和较低的潜在信息含量的微卫星与tRNALys衍生的西内斯，我们建议避免使用它们作为遗传标记。
The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes. Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.
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影响因子：
4.9
作者：
Davis, CS;Strobeck, C
通讯作者：
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