Bouwman Aniek C, Derks Martijn F L, Broekhuijse Marleen L W J, Harlizius Barbara, Veerkamp Roel F
Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
Topigs Norsvin Research Center, 6640 AA, Beuningen, The Netherlands.
BMC Genomics. 2020 Aug 24;21(1):576. doi: 10.1186/s12864-020-06989-x.
A balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without any loss or gain of DNA in germline cells. Carriers of balanced RTs are viable individuals with no apparent phenotypical consequences. These animals produce, however, unbalanced gametes and show therefore reduced fertility and offspring with congenital abnormalities. This cytogenetic abnormality is usually detected using chromosome staining techniques. The aim of this study was to test the possibilities of using paired end short read sequencing for detection of balanced RTs in boars and investigate their breakpoints and junctions.
Balanced RTs were recovered in a blinded analysis, using structural variant calling software DELLY, in 6 of the 7 carriers with 30 fold short read paired end sequencing. In 15 non-carriers we did not detect any RTs. Reducing the coverage to 20 fold, 15 fold and 10 fold showed that at least 20 fold coverage is required to obtain good results. One RT was not detected using the blind screening, however, a highly likely RT was discovered after unblinding. This RT was located in a repetitive region, showing the limitations of short read sequence data. The detailed analysis of the breakpoints and junctions suggested three junctions showing microhomology, three junctions with blunt-end ligation, and three micro-insertions at the breakpoint junctions. The RTs detected also showed to disrupt genes.
We conclude that paired end short read sequence data can be used to detect and characterize balanced reciprocal translocations, if sequencing depth is at least 20 fold coverage. However, translocations in repetitive areas may require large fragments or even long read sequence data.
平衡性染色体相互易位（RT）是两条非同源染色体末端片段的相互交换，在生殖细胞中DNA没有任何丢失或增加。平衡性RT的携带者是有活力的个体，没有明显的表型后果。然而，这些动物会产生不平衡的配子，因此生育力降低，后代会出现先天性异常。这种细胞遗传学异常通常使用染色体染色技术进行检测。本研究的目的是测试使用双末端短读长测序检测公猪中平衡性RT的可能性，并研究其断点和连接点。
在一项盲法分析中，使用结构变异检测软件DELLY，通过30倍短读长双末端测序，在7个携带者中的6个中检测到了平衡性RT。在15个非携带者中未检测到任何RT。将覆盖度降低到20倍、15倍和10倍表明，至少需要20倍的覆盖度才能获得良好的结果。在盲筛中未检测到一个RT，然而，在解除盲法后发现了一个极有可能的RT。这个RT位于一个重复区域，显示了短读长序列数据的局限性。对断点和连接点的详细分析表明，有三个连接点显示出微同源性，三个连接点为平端连接，在断点连接点处有三个微插入。检测到的RT也显示会破坏基因。
我们得出结论，如果测序深度至少为20倍覆盖度，双末端短读长序列数据可用于检测和表征平衡性相互易位。然而，重复区域中的易位可能需要大片段甚至长读长序列数据。
