Tandem Repeats in the Genome of Sus scrofa, Their Localization on Chromosomes and in the Spermatogenic Cell Nuclei

Abstract

Bioinformatics methods make it possible to find and annotate large tandem repeats (TR) in the genome assemblies of different organisms. In this study, the genomic assembly of Sus scrofa (pig) (Sscrofa10.2, in the NCBI database) was examined and a set of species-specific TR was identified. In addition, using FISH and the designed short oligonucleotide probes (Sscrf_335A, Sscrf_243A, Sscrf_15A, and Sscrf_50A), some of these TR were mapped to metaphase chromosomes. All TR present in the Repbase database for pig are detected using bioinformatics methods, and in addition to these, another 18 new TR families were found in the genome assembly Sscrofa10.2. Compared to human and mouse, the set of TR identified in the Sscrofa10.2 assembly is characterized by longer monomer length. The Sscrf_15A and Sscrf_243A probes identify a set of acrocentric (Ac) chromosomes, the Sscrf_50A probe identifies a set of sub/metacentric (Mc) chromosomes, and the Sscrf_335A probe labels all chromosomes. Probes were used to follow the centromeric region organization during spermatogenesis. In meiotic prophase I, all probes labeled ring structures, which were not described in the literature. In this study it was demonstrated that (1) the designed probes detected the Ms and Ac chromosome sets; (2) in spermatozoa, there was a specific pattern for each probe; and (3) centromeric probes probably provided an opportunity to follow the centromeric region arrangement.