Using short read sequencing to characterise balanced reciprocal translocations in pigs
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RESEARCH ARTICLE
Open Access
Using short read sequencing to characterise balanced reciprocal translocations in pigs Aniek C. Bouwman1* , Martijn F. L. Derks1,2, Marleen L. W. J. Broekhuijse2, Barbara Harlizius2 and Roel F. Veerkamp1
Abstract Background: 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. Results: 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. Conclusions: 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. Keywords: Karyotype, Pig, Reciprocal translocation, Whole genome sequencing
Background In diploid mammals, a normal karyotype consist of two copies of each chromosome. Unfortunately, various unbalanced constitutional abnormal karyotypes have been observed in unviable offspring and individuals with * Correspondence: [email protected] 1 Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands Full list of author information is available at the end of the article
various clinical disorders. In contrast, balanced constitutional chromosomal abnormalities usually result in viable individuals with no apparent phenotypical consequences, except for reduced fertility. Balanced chromosomal abnormalities, such as reciprocal translocations (RT), have no gain or loss of chromosomal material. Hence, all required genes to function properly are present, unless the breakpoints disrupt such genes.
© The Author(s). 2020 Open Access This article is licensed under a Creati
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