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

Edward S. Rice, Sergey Koren, Arang Rhie, Michael P. Heaton, Theodore S. Kalbfleisch, Timothy Hardy, Peter H. Hackett, Derek M. Bickhart, Benjamin D. Rosen, Brian Vander Ley, Nicholas W. Maurer, Richard E. Green, Adam M. Phillippy, Jessica L. Petersen, Timothy P.L. Smith

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

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.

Original languageEnglish
Article numbergiaa029
JournalGigaScience
Volume9
Issue number4
DOIs
StatePublished - Apr 6 2020

Bibliographical note

Funding Information:
This work was supported by ARS Project No. 3040-32000-034-00D. E.S.R. and sample collection costs were supported by funding from an Enhanced Research Collaboration grant from the University of Nebraska–Lincoln, Institute of Agriculture and Natural Resources, Agricultural Research Division and the USDA Meat Animal Research Center. D.M.B. was supported by USDA CRIS project No. 5090-31000-026-00-D. S.K., A.R., and A.M.P. were supported by the Intramural Research Program of the Na- tional Human Genome Research Institute, National Institutes of Health. A.R. was also supported by the Korean Visiting Scientist Training Award (KVSTA) through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health AND Welfare (HI17C2098).

Funding Information:
This work was supported by ARS Project No. 3040-32000-034- 00D. E.S.R. and sample collection costs were supported by funding from an Enhanced Research Collaboration grant from the University ofNebraska-Lincoln, Institute of Agriculture and Natural Resources, Agricultural Research Division and the USDA Meat Animal Research Center.

Publisher Copyright:
© 2020 The Author(s) 2020.

Keywords

  • Bos grunniens
  • Bos taurus
  • Highland cattle
  • genome assembly
  • phasing

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

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