ArticlePloS one2012
Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.Scientific reports · 2023Article
- Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data.International journal of molecular sciences · 2021Article
- The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock.Genes · 2020Review
- Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candidate causal mutation.Genetics, selection, evolution : GSE · 2018Article
- Characterization of recombination features and the genetic basis in multiple cattle breeds.BMC genomics · 2018Article
- CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations.GigaScience · 2017Article
- Unraveling the message: insights into comparative genomics of the naked mole-rat.Mammalian genome : official journal of the International Mammalian Genome Society · 2016Review
- Extracting functional trends from whole genome duplication events using comparative genomics.Biological procedures online · 2016Review
- A clone-free, single molecule map of the domestic cow (Bos taurus) genome.BMC genomics · 2015Article
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
- A new rhesus macaque assembly and annotation for next-generation sequencing analyses.Biology direct · 2014Article
- RepARK--de novo creation of repeat libraries from whole-genome NGS reads.Nucleic acids research · 2014Article
- The challenges and importance of structural variation detection in livestock.Frontiers in genetics · 2014Review
- RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.Frontiers in immunology · 2014Article
- A genome-wide scan for signatures of differential artificial selection in ten cattle breeds.BMC genomics · 2013Article
- Genetic variants and signatures of selective sweep of Hanwoo population (Korean native cattle).BMB reports · 2013Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We analyzed the whole genome sequence coverage in two versions of the Bos taurus genome and identified all regions longer than five kilobases (Kbp) that are duplicated within chromosomes with >99% sequence fidelity in both copies. We call these regions High Fidelity Duplications (HFDs). The two assemblies were Btau 4.2, produced by the Human Genome Sequencing Center at Baylor College of Medicine, and UMD Bos taurus 3.1 (UMD 3.1), produced by our group at the University of Maryland. We found that Btau 4.2 has a far greater number of HFDs, 3111 versus only 69 in UMD 3.1. Read coverage analysis shows that 39 million base pairs (Mbp) of sequence in HFDs in Btau 4.2 appear to be a result of a mis-assembly and therefore cannot be qualified as segmental duplications. UMD 3.1 has only 0.41 Mbp of sequence in HFDs that are due to a mis-assembly.
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