Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle.

Autor: Rice ES; Department of Animal Science, University of Nebraska-Lincoln, C203 ANSC, Lincoln, NE 68583, USA.; Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA., Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA., Rhie A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA., Heaton MP; US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA., Kalbfleisch TS; Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA., Hardy T; USYAKS, Livermore, CO 80536, USA., Hackett PH; USYAKS, Livermore, CO 80536, USA., Bickhart DM; Dairy Forage Research Center, 1925 Linden Drive, ARS USDA, Madison, WI 53706, USA., Rosen BD; Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave., ARS USDA, Beltsville, MD 20705, USA., Ley BV; Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, 820 Road 313, Clay Center, NE 68933, USA., Maurer NW; Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA., Green RE; Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA., Phillippy AM; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA., Petersen JL; Department of Animal Science, University of Nebraska-Lincoln, C203 ANSC, Lincoln, NE 68583, USA., Smith TPL; US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA.
Jazyk: angličtina
Zdroj: GigaScience [Gigascience] 2020 Apr 01; Vol. 9 (4).
DOI: 10.1093/gigascience/giaa029
Abstrakt: Background: The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes.
Results: We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present.
Conclusions: The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.
(© The Author(s) 2020. Published by Oxford University Press.)
Databáze: MEDLINE
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