An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome

Kimberly M. Davenport, Derek M. Bickhart, Kim Worley, Shwetha C. Murali, Mazdak Salavati, Emily L. Clark, Noelle E. Cockett, Michael P. Heaton, Timothy P.L. Smith, Brenda M. Murdoch*, Benjamin D. Rosen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)


Background: The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. Findings: Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI-Ramb-v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar-rambouillet-v1.0 and Oar-v4.0. ARS-UI-Ramb-v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. Conclusions: The ARS-UI-Ramb-v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep.

Original languageEnglish
Article numbergiab096
Early online date4 Feb 2022
Publication statusPrint publication - 4 Feb 2022
Externally publishedYes

Bibliographical note

© The Author(s) 2022. Published by Oxford University Press GigaScience.


  • genome assembly
  • Ovis aries
  • Rambouillet
  • reference genome
  • sheep
  • Sheep/genetics
  • Animals
  • Molecular Sequence Annotation
  • High-Throughput Nucleotide Sequencing
  • Genome
  • Chromosomes
  • Whole Genome Sequencing


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