Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.
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DOI：
10.1093/nar/gkv1193
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发表时间：
2015-12-15
影响因子：
14.9
通讯作者：
Lau NC
中科院分区：
文献类型：
--
作者：
Rahman R;Chirn GW;Kanodia A;Sytnikova YA;Brembs B;Bergman CM;Lau NC
为了了解转座子景观（TL）如何在动物基因组中变化，我们描述了一种名为转座子插入和耗尽分析器（TIDAL）的新方法和果蝇（TIDAL-Fly）中超过300个TL的数据库。我们的分析揭示了细胞系和果蝇品系之间普遍存在的TL多样性，即使是来自不同实验室的同名亚株，如用于参考基因组序列的ISO 1菌株。平均而言，在每个实验室品系、果蝇遗传参考组（DGRP）的近交品系和果蝇基因组连接（DGN）中的果蝇分离株中存在>500个新插入。少数（<25%）转座子家族构成了果蝇品系间TL多样性的大部分（>70%）。插入和耗尽模式之间的鲜明对比表明，许多转座子是唯一的ISO 1参考基因组序列。虽然从苍蝇株TL多样性达到渐近极限，增加测序深度，猖獗的TL多样性导致不饱和的检测池中的苍蝇的TL。最后，我们发现新的转座子插入与大多数转座子家族的Piwi相互作用RNA（皮尔纳）水平呈负相关，除了高度丰富的roo反转录转座子。我们的研究为果蝇遗传学家了解转座子如何在果蝇细胞系和品系中创造广泛的基因组多样性提供了有用的资源。
To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.