ARS | Publication request: Differential Turn-over Patterns of Transposable Elements Account for the Genome Size Differences among Cattle, Dog and Human.

Submitted to: CONFERENCE ON THE BIOLOGY OF GENOMES
Publication Type: Abstract
Publication Acceptance Date: May 15, 2006
Publication Date: May 10, 2006
Citation: Liu, G., Matukumalli, L.K., Sonstegard, T.S., Van Tassell, C.P. 2006. Differential turn-over patterns of transposable elements account for the genome size differences among cattle, dog and human. (abstract) Conference on the Biology off Genomes, pp 187.

Technical Abstract: A large-scale comparative genome analysis was performed on 11 Mb of high-quality finished genomic sequence from cattle, dog, and human to estimate the pattern, frequency, and nature of transposable elements and their contribution to the whole genome size. Even though the length of unique portions of genomic sequence remained relatively constant, 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 proportion of transposable elements recognizable in dog (28.9%), cattle (39.5%) and human (45.6%). Differential turn-over patterns of lineage-specific or ancestral transposable elements were found to account for the overall size differences among cattle, dog and human genomes. The smaller size of the cattle genome relative to human is primarily due to less ancestral repeat sequences, indicating a larger loss in ancestral LINE and LTR elements in cattle. The total lengths of lineage-specific repeats were approximately the same in cattle and human, even though these elements differ in their types, frequencies and lengths. The larger size of the cattle genome 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. The deletion of ancestral repeats was slightly higher in cattle than in dog; however, the contribution was minimal. Alternatively, both lineage-specific repeat sequences and ancestral repeat sequences contributed to the larger size of the human genome as compared to dog. This difference reflects a higher insertion activity, longer insertion elements, and lower deletion activity of ancestral repeats in human. Assuming an ancestral genome size of 2.8 Gb and that deletions occur continually, the rate of genomic deletion has been approximately 8.4% and 29% higher in cattle than in the dog and human lineages.