Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions
Sequence-Based Detection and Breakpoint Assembly of Polymorphic Inversions
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DOI：
10.1534/genetics.112.141622
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发表时间：
2012-09-01
期刊：
影响因子：
3.3
通讯作者：
Langley, Charles H.
中科院分区：
文献类型：
--
作者：
Corbett-Detig, Russell B.;Cardeno, Charis;Langley, Charles H.
倒置多态性自20世纪20年代被发现以来，在果蝇遗传研究中一直占据着特殊的地位。事实上，倒位似乎几乎无处不在，并且已经被彻底调查的大多数物种都被发现具有一个或多个染色体倒位的多态性。然而，尽管持续的兴趣，反转仍然难以研究，因为它们的影响往往是神秘的，并且很少有有效的测定方法被开发出来。即使在可以可靠地检测反转并受到相当关注的果蝇中，也只有三个反转的断点被分子表征。因此，反演检测和分析设计仍然是重要的未解决的问题。在这里，我们提出了一种方法来识别和局部从头组装的反转断点利用新一代的配对末端读取来自D. melanogaster等雌性系。PCR和细胞学验证表明，我们的方法可以可靠地组装反转断点，为今后的研究提供了工具，也为不同类群的反转和其他染色体畸变的检测和分析设计提供了框架。
Inversion polymorphisms have occupied a privileged place in Drosophila genetic research since their discovery in the 1920s. Indeed, inversions seem to be nearly ubiquitous, and the majority of species that have been thoroughly surveyed have been found to be polymorphic for one or more chromosomal inversions. Despite enduring interest, however, inversions remain difficult to study because their effects are often cryptic, and few efficient assays have been developed. Even in Drosophila melanogaster, in which inversions can be reliably detected and have received considerable attention, the breakpoints of only three inversions have been characterized molecularly. Hence, inversion detection and assay design remain important unsolved problems. Here, we present a method for identification and local de novo assembly of inversion breakpoints using next-generation paired-end reads derived from D. melanogaster isofemale lines. PCR and cytological confirmations demonstrate that our method can reliably assemble inversion breakpoints, providing tools for future research on D. melanogaster inversions as well as a framework for detection and assay design of inversions and other chromosome aberrations in diverse taxa.