ArticleNature communications2020
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 171 citations in OpenAlex.
- A High-Quality Haplotype-Resolved Reference Genome for Drakensberger Cattle (Bos taurus indicus/taurus) Achieved Through Trio-Binned Long-Read Sequencing.Scientific data · 2026Article
- Comparative analysis of microRNAs in bovine colostrum and neonatal calf blood.Journal of the science of food and agriculture · 2026Article
- Polymorphism in the TLR Adaptors of the Toll Signalling Pathway for Use in Livestock Breeding for Health Traits.International journal of molecular sciences · 2026Review
- Article
- Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.Animal genetics · 2026Article
- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics.Biology · 2026Review
- The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution.Animals : an open access journal from MDPI · 2026Review
- A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba.GigaScience · 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
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- Genome assemblies of IndianNAR genomics and bioinformatics · 2025Article
- Review
- Insights into natural neocentromere evolution from a cattle T2T X chromosome.Nature communications · 2025Article
- Comprehensive detection of structural variations in long and short reads dataset of French cattle.Scientific reports · 2025Article
- Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.Molecular biology and evolution · 2025Article
- Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs.Nature communications · 2025Article
- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake.Molecular biology and evolution · 2025Article
- Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.Science China. Life sciences · 2025Review
25 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 11 institutions in 3 countries.
Funding
Abstract
Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.
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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.