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Title: Analysis of recent segmental duplications in the bovine genome

item Liu, Ge - George
item VENTURA, MARIO - University Of Bari
item CELLAMARE, ANGELO - University Of Bari
item CHEN, LIN - University Of Washington
item CHENG, ZE - University Of Washington
item ZHU, BIN - University Of Maryland
item SONG, JIUZHOU - University Of Maryland
item EICHLER, EVEN - University Of Washington

Submitted to: Gordon Research Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/14/2009
Publication Date: 7/19/2009
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.

Interpretive Summary:

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.