A universal method for the study of CR1 retroposons in nonmodel bird genomes.
A universal method for the study of CR1 retroposons in nonmodel bird genomes.
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DOI：
10.1093/molbev/mss124
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发表时间：
2012-10
影响因子：
10.7
通讯作者：
Alexander Suh;J. Kriegs;S. Donnellan;J. Brosius;J. Schmitz
中科院分区：
文献类型：
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作者：
Alexander Suh;J. Kriegs;S. Donnellan;J. Brosius;J. Schmitz
逆转录酶插入的存在/不存在模式在orthopathic基因组位点构成系统发育或群体遗传学研究的直接标记。在鸟类中，这些标记的方便鉴定和应用迄今为止主要限于导致模式鸟的谱系（即，鸡和斑胸草雀）。我们提出了一种易于使用，快速，成本效益高的方法，实验分离鸡重复1（CR 1）插入几乎任何鸟类基因组和潜在的nonavian基因组。我们的方法的应用程序，小grebe基因组产生的插入属于新的CR 1亚科，分散在整个鸟类CR 1 s的系统发育树。此外，这些插入的存在/不存在的分析提供了第一个逆转录酶证据分组火烈鸟+ grebes Mirandornithes和几个标记的所有后续分支事件grebes（Podicipediformes）。五个标记似乎是物种特异性插入，包括迄今为止的第一个证据，在鸟类的双等位基因CR 1插入，可能是有用的，在未来的人口遗传学研究。
Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.