Genomic organization and evolution of the ULBP genes in cattle

Larson, Joshua H.; Marron, Brandy M.; Beever, Jonathan E.; Roe, Bruce A.; Lewin, Harris A.

doi:10.1186/1471-2164-7-227

Cited by 25 publications

(16 citation statements)

References 33 publications

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“…Finally, gene conversion has played a major role in shaping the IFNA gene family in eutherian species after gene duplication [ 44 , 45 ]. The other duplication examples include TCRV [ 46 ], C-type lysozymes [ 29 ], BPI-like ( BSP30 ) [ 47 ], BPI / LBP , Cathelicidin [ 29 ], interferon subfamilies ( IFNB , IFNW , and IFNX ) [ 29 ], Pregnancy-associated glycoprotein [ 48 ], Sulfotransferases, ULBP [ 49 ], WC1 [ 50 ] and etc.…”

Section: Resultsmentioning

confidence: 99%

Analysis of recent segmental duplications in the bovine genome

Liu¹,

et al. 2009

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BackgroundDuplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (≥ 1 kb in length, ≥ 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes.ResultsIn this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently 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. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction.ConclusionOur results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.

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Section: Resultsmentioning

confidence: 99%

Analysis of recent segmental duplications in the bovine genome

Liu¹,

et al. 2009

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“…To highlight the potential evolutionary contributions of these CNVs to cattle breed formation and adaptation, we conservatively queried out 35 CNVRs that have high-confidence breed-specific CNV frequency differences (Supplemental Table S12). Twenty-nine of these CNVRs correspond to annotated genes or gene families, while many of them are also known in other mammals to interact with environments, some of them are known to be important in cattle adaptation including SCP2 (Liu et al 2009), ULBP (Larson et al 2006), and WC1.1 (Herzig and Baldwin 2009). To our knowledge, this is the first systematic report on breed-specific copy number differences in cattle.…”

Section: Cattle Cnv Frequency Differences Among Breedsmentioning

confidence: 99%

“…4; Supplemental Table S13). After mapping of the ULBP major cluster (Larson et al 2006), we found within this region ULBP21 and ULBP2 are potential functional copies, while other copies are either partially overlapped (ULBP17 ) or pseudogenes (Supplemental Fig. S4).…”

Section: Cattle Cnv Frequency Differences Among Breedsmentioning

confidence: 99%

Analysis of copy number variations among diverse cattle breeds

Liu¹,

Hou²,

Zhu³

et al. 2010

Genome Res.

263

318

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Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here, we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, three Bos indicus, and three composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 megabases or ;1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

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“…Mapped ULBP genes are all assigned to a 3.1 Mb region on chromosome 9. The organization of the ULBP gene cluster in the Hereford cattle differs from that of the Holstein cattle , both in terms of gene copy number and arrangement. Therefore, ULBP genes seem to display copy number variations across diverse breeds .…”

Section: Comparative Genomics Of the Ulbp Gene Familymentioning

confidence: 96%

Comparative genomics of the NKG2D ligand gene family

Kasahara

Sutoh

2015

Immunological Reviews

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NKG2D ligands (NKG2DLs) are a group of stress-inducible major histocompatibility complex (MHC) class I-like molecules that act as a danger signal alerting the immune system to the presence of abnormal cells. In mammals, two families of NKG2DL genes have been identified: the MIC gene family encoded in the MHC region and the ULBP gene family encoded outside the MHC region in most species. Some mammals have a third family of NKG2DL-like class I genes which we named MILL (MHC class I-like located near the leukocyte receptor complex). Despite the fact that MILL genes are more closely related to MIC genes than ULBP genes are to MIC genes, MILL molecules do not function as NKG2DLs, and their function remains unknown. With the progress of mammalian genome projects, information on the MIC, ULBP, and MILL gene families became available in many mammalian species. Here, we summarize such information and discuss the origin and evolution of the NKG2DL gene family from the viewpoint of host-pathogen coevolution.

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Genomic organization and evolution of the ULBP genes in cattle

Cited by 25 publications

References 33 publications

Analysis of recent segmental duplications in the bovine genome

Analysis of recent segmental duplications in the bovine genome

Analysis of copy number variations among diverse cattle breeds

Comparative genomics of the NKG2D ligand gene family

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