ArticleNature communications2023
De novo genome assembly depicts the immune genomic characteristics of cattle.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Comparative analysis of the organization and complexity of immunoglobulin light chain loci in equids.Journal of animal science · 2026Article
- High-throughput profiling of the T cell receptor delta CDR3 repertoire reveals species-specific patterns in cattle (Bos taurus) and water buffalo (Bubalus bubalis).Frontiers in immunology · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Genome assembly and structural variations of Guyuan cattle.Scientific data · 2025Article
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- From benchmarking alignment of genome assemblies to IMGT annotation: the paradigm of the bovine Bos taurus T cell receptor (TRG) locus.BMC genomics · 2025Article
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.Molecular biology and evolution · 2025Article
- CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies.Genome biology · 2025Article
- SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants.Nature communications · 2025Article
- A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research.GigaScience · 2025Article
- Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality.GigaScience · 2024Article
- Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Frontiers in immunology · 2024Article
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.
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