Simple Sequence Repeats in the Bovine, Human and Canine Genomes
Simple sequence repeats (SSRs) are desirable markers in mammalian genomic studies. Due to their instability, they are often highly polymorphic and can be used in related species. The Baylor HGSC 6.3X assembly of the bovine genome provides a resource for cattle SSR identification and characterisation. The results were compared to the dog and human genomes. Raw data was processed through the SPUTNIK program to detect SSRs of di-, tri-, tetra- and pentanucleotide classes; specifically, those over 10 bps in length in all species. Results predict that the bovine genome will contain 1,176,094 SSRs, at a density of 1 per 2423 bps. In human, 1,255,667 SSRs were identified (1 per 2465 bps) and 1,891,594 SSRs in dog (1 per 1332 bps). Estimated repeat instability, average repeat length and motif frequencies also differed between species. Human and canine SSRs appeared to be more unstable, with longer repeats observed. Number of SSRs in each class was significantly different between species, with human having more tri- and pentanucleotide SSRs than dogs; and more di- and tetranucleotide SSRs than cattle. Of trinucleotide repeats, the human genome had 10% the proportion of AGC repeats found in cattle and 97% that of dog. It is of interest that these repeats (CAG) are implicated in various human diseases, such as Huntington disease and spinocerebellar ataxia. Interestingly, 23% of di- and 68% of trinucleotide bovine repeats have flanking artiodactyl specific SINE elements, suggesting their involvement in repeat generation/contraction. The SINE elements were preferentially located adjacent to AGC repeats. In conclusion, three mammalian genomes have been compared and marked species specific differences in SSRs were observed. This suggests variability in the mechanisms involved in the creation, maintenance and loss of these class of sequences in mammals.