ArticleNature communications2022
Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed, 82 citations in OpenAlex.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Resolving Cattle GWAS Loci: Current Progress, Persistent Challenges and Future Directions.Current issues in molecular biology · 2026Review
- Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.Nature communications · 2026Article
- A comparative study on recombination activity in cattle.Genetics, selection, evolution : GSE · 2026Article
- Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.Animal genetics · 2026Article
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity.Journal of animal science and biotechnology · 2026Article
- Article
- Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.Nature communications · 2026Article
- Molecular QTL are enriched for structural variants in a cattle long-read cohort.Communications biology · 2026Article
- The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Opportunities and computational challenges in large-scale whole-genome sequencing data analysis.Journal of animal science · 2026Review
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- Genome assemblies of IndianNAR genomics and bioinformatics · 2025Article
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.Genetics, selection, evolution : GSE · 2025Article
- A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (II) Fast One-Step Assembly of Highly Continuous Chromosome Sequences.Animals : an open access journal from MDPI · 2025Article
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
- Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens.iMetaOmics · 2025Article
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Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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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.