Erratum to: A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.
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ABSTRACT:
SUBMITTER: Heaton MP
PROVIDER: S-EPMC8558578 | biostudies-literature | 2021 Aug
REPOSITORIES: biostudies-literature
Publications
Erratum to: A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.
Heaton Michael P MP Smith Timothy P L TPL Bickhart Derek M DM Vander Ley Brian L BL Kuehn Larry A LA Oppenheimer Jonas J Shafer Wade R WR Schuetze Fred T FT Stroud Brad B McClure Jennifer C JC Barfield Jennifer P JP Blackburn Harvey D HD Kalbfleisch Theodore S TS Davenport Kimberly M KM Kuhn Kristen L KL Green Richard E RE Shapiro Beth B Rosen Benjamin D BD
The Journal of heredity 20211101 6
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Project description:This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations.
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Project description:BackgroundThe genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods.ResultsWe have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions.ConclusionsBy using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome.
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