Distinct Turn-Over Patterns of Common Repeats Correlate with Genome Size Differences Among Cattle, Dog and Human

Optimal three-way global sequence alignments for 84 cattle clones or loci (total 11 Mb of high-quality finished genomic sequence, each larger than 50 kb) were constructed using the human and dog genome assemblies. Although unique portions of genomic sequence remained relatively constant among these three mammals, the overall size differences in cattle-dog, human- cattle, and human-dog comparisons were 10.6%, 6.2%, and 16.8% respectively, which strongly correlated with the difference between repetitive portions in dog (28.9%), cattle (39.5%) and human (45.6%). These alignments were therefore examined for the pattern, frequency, and nature of common repeats and their contribution to the genome size. This comparison indicated that distinct turn-over patterns of lineage-specific (young) or ancestral (old) repeats may account for a repeat-driven genome size change in cattle, dog and human. The smaller size of the cattle sequence relative to human is primarily due to less ancestral repeats, indicating a larger loss of them in cattle. The larger size of the cattle sequence as compared to dog is mainly due to additional lineage specific repeat sequences in cattle, suggesting a higher insertion rate and longer lineage-specific repeats in cattle. Finally, both insertions of lineage-specific repeats and retentions of ancestral repeats contributed to the larger size of the human sequence as compared to dog. Assuming that the sampled genome sequence is representative, these differences may lead to 6-16% differences of dog, cattle, human genome size, with majorities of them due to insertions and deletions of common repeats.