Naturally occurring diseases in dogs provide an important animal model for studying human disease including cancer, heart disease, and autoimmune disorders. Transposable elements (TEs) make up ~ 31% of the dog (Canis lupus familiaris) genome and are one of main drivers to cause genomic variations and alter gene expression patterns of the host genes, which could result in genetic diseases. To detect structural variations (SVs), we conducted whole-genome sequencing of three different breeds, including Maltese, Poodle, and Yorkshire Terrier. Genomic SVs were detected and visualized using BreakDancer program. We identified a total of 2328 deletion SV events in the three breeds compared with the dog reference genome of Boxer. The majority of the genetic variants were found to be TE insertion polymorphism (1229) and the others were TE-mediated deletion (489), non-TE-mediated deletion (542), simple repeat-mediated deletion (32), and other indel (36). Among the TE insertion polymorphism, 286 elements were full-length LINE-1s (L1s). In addition, the 49 SV candidates located in the genic regions were experimentally verified and their polymorphic rates within each breed were examined using PCR assay. Polymorphism analysis of the genomic variants revealed that some of the variants exist polymorphic in the three dog breeds, suggesting that their SV events recently occurred in the dog genome. The findings suggest that TEs have contributed to the genomic variations among the three dog breeds of Maltese, Poodle, and Yorkshire Terrier. In addition, the polymorphic events between the dog breeds indicate that TEs were recently retrotransposed in the dog genome.

中文翻译：

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使用全基因组测序对狗品种进行转座子介导的结构变异分析。

狗中自然发生的疾病为研究包括癌症，心脏病和自身免疫性疾病在内的人类疾病提供了重要的动物模型。转座因子（TEs）占犬基因组的31％，是导致基因组变异和改变宿主基因的基因表达方式的主要驱动力之一，这可能导致遗传疾病。为了检测结构变异（SV），我们对三种不同的品种，包括马耳他，贵宾犬和约克夏犬进行了全基因组测序。使用BreakDancer程序检测并可视化了基因组SV。与Boxer的狗参考基因组相比，我们在这三个品种中共鉴定了2328个缺失SV事件。发现大多数遗传变异是TE插入多态性（1229），其他是TE介导的缺失（489），非TE介导的缺失（542），简单重复介导的缺失（32）和其他插入缺失。 （36）。在TE插入多态性中，有286个元素是全长LINE-1（L1s）。此外，通过实验验证了位于基因区的49个SV候选基因，并使用PCR测定法检查了每个品种内它们的多态性率。对基因组变体的多态性分析显示，在三个犬种中某些变体存在多态性，表明它们的SV事件最近在犬基因组中发生。这些发现表明，TEs促进了马耳他，贵宾犬和约克夏犬三个犬种的基因组变异。此外，