ArticleGenome biology2007
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 110 citations in OpenAlex.
- Recent advances in the genomic resources for sheep.Mammalian genome : official journal of the International Mammalian Genome Society · 2023Review
- Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep.Animals : an open access journal from MDPI · 2023Article
- Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes.Genetics, selection, evolution : GSE · 2022Review
- Evolution of the sheep industry and genetic research in the United States: opportunities for convergence in the twenty-first century.Animal genetics · 2021Review
- Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep.Molecular biology and evolution · 2017Article
- Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.Heredity · 2016Article
- Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates.PloS one · 2016Article
- Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds.BMC genomics · 2015Article
- Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep.PloS one · 2015Article
- Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012.Animal genetics · 2014Review
- The utility of low-density genotyping for imputation in the Thoroughbred horse.Genetics, selection, evolution : GSE · 2014Article
- Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.Genetics · 2013Article
- Genome-wide genetic diversity and differentially selected regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep.PloS one · 2013Article
- A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome.The Journal of physiology · 2012Article
- A critical role for increased labile zinc in reducing sensitivity of cultured sheep pulmonary artery endothelial cells to LPS-induced apoptosis.American journal of physiology. Lung cellular and molecular physiology · 2012Article
- A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.Marine biotechnology (New York, N.Y.) · 2012Article
- Advanced comparative cytogenetic analysis of X chromosomes in river buffalo, cattle, sheep, and human.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2012Article
- Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition.BMC genetics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIs it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?
resultsA sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.
conclusionWe demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.