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Title:   Author  item
                                            Liu, Ge

                                                         - *George*item
                                            VENTURA, MARIO - UNIVERSITY OF BARIitem
                                            CELLAMARE, ANGELO - UNIVERSITY OF BARIitem
                                            CHEN, LIN - UNIVERSITY OF WASHINGTONitem
                                            CHENG, ZE - UNIVERSITY OF WASHINGTONitem
                                            ZHU, BIN - UNIVERSITY OF MARYLANDitem
                                            SONG, JIUZHOU - UNIVERSITY OF MARYLANDitem
                                            EICHLER, EVEN - UNIVERSITY OF WASHINGTON
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 12/1/2009
                                    Publication  Date: 12/1/2009
                                    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. BMC Genomics. 10:571.Interpretive Summary: This a companion paper to the Bovine Genome Sequencing and Analysis Consortium paper: The Genome Sequence of Taurine Cattle: a window to ruminant biology and evolution. As a part of the effort of this consortium, we employed an integrated approach combining comparative genomics (WGAC and WSSD) and experimental verifications (FISH of 59 loci) to study the segmental duplications in the bovine genome. We describe the first systematic and genome-wide analysis of recent segmental duplications in the modern domesticated cattle (Bos taurus).  All of the experimental analyses and many computational results (chromosomal localization bias, repeat analyses, and PANTHER analyses) are the unique contribution, which are not presented in the main manuscript. We found that (1) Recent segmental duplications comprise 3.1% of the bovine genome; (2) Many linage-specific gene duplications are significantly enriched for biological functions such as immunity, rumination, lactation and reproduction with important implications in cattle speciation, adaptation and domestication; and (3) Along with rodents and carnivores, our 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. This study represents a solid advance of general interest to animal scientists and mammalian evolutionary biologists. It provides insights into mechanisms of bovine genome evolution and generates a valuable resource for accelerating genetic improvement for milk and beef production. It also provides the foundation for correlating structural variation with the molecular basis of economically important adaptive traits of ruminants such as lactation, metabolism, reproduction and disease resistance, which will be an important complement to SNP centric genome-wide association studies.  It will be the definitive citation for the first detailed analysis of cattle segmental duplications.
                                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.


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