Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Alexander S. Leonard (), Danang Crysnanto, Zih-Hua Fang, Michael P. Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy P. L. Smith, Benjamin D. Rosen () and Hubert Pausch ()
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Alexander S. Leonard: Animal Genomics, ETH Zurich
Danang Crysnanto: Animal Genomics, ETH Zurich
Zih-Hua Fang: Animal Genomics, ETH Zurich
Michael P. Heaton: U.S. Meat Animal Research Center, USDA-ARS
Brian L. Vander Ley: University of Nebraska-Lincoln
Carolina Herrera: University of Zurich
Heinrich Bollwein: University of Zurich
Derek M. Bickhart: Dairy Forage Research Center, USDA-ARS
Kristen L. Kuhn: U.S. Meat Animal Research Center, USDA-ARS
Timothy P. L. Smith: U.S. Meat Animal Research Center, USDA-ARS
Benjamin D. Rosen: Animal Genomics and Improvement Laboratory, USDA-ARS
Hubert Pausch: Animal Genomics, ETH Zurich

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: Abstract Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.

Date: 2022
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DOI: 10.1038/s41467-022-30680-2

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