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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Analysis of recent segmental duplications in the bovine genome

item Liu, Ge
item Ventura, Mario -
item Cellamare, Angelo -
item Chen, Lin -
item Cheng, Ze -
item Zhu, Bin -
item Song, Jiuzhou -
item Eichler, Even -

Submitted to: Gordon Research Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: May 14, 2009
Publication Date: July 19, 2009
Citation: Liu, G., Ventura, M., Cellamare, A., Chen, L., Cheng, Z., Zhu, B., Song, J., Eichler, E.E. 2009. Analysis of recent segmental duplications in the bovine genome. [abstract]. Gordon Research Conference Proceedings.

Technical Abstract: Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We describe the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimate that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (= 1kb in length, = 90% sequence identity). Similar to other working draft assemblies almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes, indicating that segmental duplications have been problematic for sequence and assembly of the bovine genome. We further confirmed and investigated the distribution of the largest duplications using FISH. Both experimental and computational analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. We find that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, rumination, lactation and reproduction. The level of sequence identity suggests that over 25% of these duplications have occurred within the artiodactylan or more-specifically within the Bos lineage of evolution with important implications in cattle speciation and adaptation.

Last Modified: 8/27/2016
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