ArticleGigaScience2022
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Molecular epidemiology ofMicrobiology spectrum · 2026Article
- Low-Coverage Whole-Genome Sequencing Identifies Loci Associated with Birth Weight in East Friesian × Hu Crossbred Sheep.Animals : an open access journal from MDPI · 2026Article
- Sheep erythrocyte potassium locus highlights MYADM family regulation of electroneutral potassium chloride cotransporters (KCC).BMC genomics · 2026Article
- Whole genome copy number variation analysis to detect genomic regions for resistance to Haemonchus contortus in Sheep.BMC genomics · 2026Article
- Selection signatures on the autosomes and the X chromosome in the prolific Belclare sheep breed.Veterinary and animal science · 2026Article
- Whole-genome resequencing revealed genetic diversity and the haplotype containing MC1R associated with black coat color in Liangshan sheep.BMC genomics · 2026Article
- Identification and functional assessment of CDSN gene variants associated with horn phenotypes in sheep.BMC genomics · 2026Article
- Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.Nature communications · 2026Article
- Genetic diversity of US Rambouillet in the National Sheep Improvement Program compared to other sheep breeds.The Journal of heredity · 2026Article
- A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.GigaScience · 2026Article
- Unravelling viral identity: avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses.Virus evolution · 2026Article
- Claudin and Rab proteins are key molecular components involved in coccidiosis resistance in Portuguese Merino sheep.Genetics, selection, evolution : GSE · 2025Article
- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- Candidate gene search for milk production and composition, milk coagulation properties, and milk protein profile in dairy sheep from a New Zealand flock.Animal biotechnology · 2025Article
- Cross-species identification of conserved cell-type specific mechanisms during early placenta development in ruminants.Scientific reports · 2025Article
- Genome assembly and whole-genome resequencing study of Butuo Black sheep (Ovis aries).Scientific data · 2025Article
- Single-cell analysis of uterine artery endothelial cells reveals cytokine-induced emergence of specific immunomodulatory subtypes: implications for preeclampsia.Journal of molecular endocrinology · 2025Article
- Exploring skeletal disorders in cattle and sheep: a WGS-based framework for diagnosis and classification.Genetics, selection, evolution : GSE · 2025Article
- The Metabolome in Different Sites of Gut Tract Regulates the Meat Quality of Longissimus Dorsi Muscle.Animals : an open access journal from MDPI · 2025Article
- Whole genome sequencing and structural variations provide insights into the body size traits of Hu sheep.Scientific data · 2025Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
backgroundThe 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.
findingsShort-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.
conclusionsThe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.