@misc{leonard_crysnanto_fang_heaton_vander ley_herrera_bollwein_bickhart_kuhn_smith_et al._2021,
title={Bovine pangenome reveals trait-associated structural variation from diverse assembly inputs},
DOI={10.1101/2021.11.02.466900},
abstractNote={AbstractAdvantages 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. Ten haplotype-resolved assemblies of three bovine trios representing increasing levels of heterozygosity were generated that each demonstrate a substantial improvement in contiguity and accuracy over the current Bos taurus reference genome, with more telomere and centromere content and an average 2.5x increase in NG50 and 11x decrease in base errors. Downsampling analysis demonstrated that diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. The assemblies were integrated into structural variant-based pangenomes that demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified approximately 900 structural variants overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46 and GC that have potential to affect phenotype.},
publisher={Cold Spring Harbor Laboratory},
author={Leonard, Alexander S. and Crysnanto, Danang and Fang, Zih-Hua and Heaton, Michael P and Vander Ley, Brian L. and Herrera, Carolina and Bollwein, Heinrich and Bickhart, Derek M. and Kuhn, Kristen L. and Smith, Timothy PL. and et al.},
year={2021},
month={Nov}
}