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

Tandem Repeat-Based Probes Support the Loop Model of Pericentromere Packing

“…This family is similar to the previously cloned SSAT repeat [Janzen et al, 1999]. The cloned repeat was localized at the CEN of chromosome 9, suggesting its chromosome specificity [Janzen et al, 1999]; however, in silico, this repeat was found on more chromosomes [Ivanova et al, 2019]. Among the newly identified repeats, the Sscrf_243A repeat, which was relatively rich in GC content (59%), demonstrated no similarity to the dispersed repeats but possibly possessed chromosome specificity, determined in silico, and was located on chromosome 5.…”

“…The rings could result from CEN associations of different chromosomes or could belong to each individual chromosome. To test these hypotheses, we took into account the ratio between the number of signals in spermatocytes and spermatozoa and that on the metaphase plates [Ivanova et al, 2019]. The number of signals varied depending on the hybridization efficiency, and the weak signals did not appear regularly.…”

“…The search for large TR in genome assemblies (APMK for hamster; AEMK01 [Sscrofa10.2] and AEMK02 [Sscrofa11.1] for pig) was described in detail previously [Komissarov et al, 2011]. Computation of short oligonucleotide probes for FISH and probe testing on metaphase plates was also described [Komissarov et al, 2011;Ivanova et al, 2019]. TR length was measured by aligning reads from runs at fields of certain TR family by Bowtie2 with the sensitivity parameter "local" as described before [Miheev et al, 2015], with the percentage of aligned reads converted to nucleotide pairs based on the length of whole-genome shotgun (WGS) sequences.…”

“…The Sscrf-335A (SSAT_A/SSAT_B in Repbase) and Sscrf-50A (SAT-1_SSc in Repbase) belong to periCEN chromatin of metacentric chromosomes. The Sscrf-15A (SSRS2 in Repbase) and Sscrf-243A reside at peri-CEN chromatin of acrocentric chromosomes [Ivanova et al, 2019]. The oligonucleotide probe sequences used for FISH analysis are presented below:…”

“…So, initially we describe the localization of most probes as centromeric in a broad sense, meaning that they are situated in the region of primary constriction but their precise location is unknown. The probes used in the present study for TR are considered as periCEN because they exhibit a relative chromosome specificity [Ivanova et al, 2019]. The same techniques were used to study a poorly assembled genome of the hamster Mesocricetus auratus [Miheev et al, 2015] and the Chinese hamster Cricetulus griseus.…”