ArticleGenome research2023
The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 27 citations in OpenAlex.
- Pre-divergence hybridization and adaptive introgression shaped the genetic architecture of East Asian domestic pigs.Science China. Life sciences · 2026Article
- Understanding the structure of swine leukocyte antigen class I molecules.Cellular & molecular biology letters · 2026Review
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Retrotransposed gene copies persist under relaxed selection in wild Spodoptera frugiperda.Molecular biology and evolution · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Chromosome-level genome assembly of two Chinese wild boars (Sus scrofa).Scientific data · 2026Article
- Review
- De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.Biomolecules · 2026Article
- Advancements in Animal Breeding: From Mendelian Genetics to Machine Learning.International journal of molecular sciences · 2025Review
- 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
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- APAV: An advanced pangenome analysis and visualization toolkit.PLoS computational biology · 2025Article
- Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Exploration of gene presence/absence variations inOpen biology · 2025Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression.Journal of animal science and biotechnology · 2024Article
- The goat pan-genome reveals patterns of gene loss during domestication.Journal of animal science and biotechnology · 2024Article
- Article
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Authors and funding
19 authors at 4 institutions in 2 countries.
Funding
Abstract
Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.
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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.