ArticleiScience2023
Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.
Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 44 citations in OpenAlex.
- Research evolution of flat peach (Frontiers in plant science · 2025Pooled it
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Review
- De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.Biomolecules · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 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
- Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Constructing a draft Indian cattle pangenome using short-read sequencing.Communications biology · 2025Article
- Application of Omics in Donkey Meat Research: A Review.Animals : an open access journal from MDPI · 2025Review
- Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.BMC biology · 2025Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement.Nature genetics · 2025Article
- Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms.Animals : an open access journal from MDPI · 2025Article
- A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.GigaScience · 2025Article
Corrections and comments
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Authors and funding
16 authors at 6 institutions in 2 countries.
Funding
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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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.