ArticleGigaScience2025
A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research.
Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- 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
- A standardised and reproducible method forAnnals of translational medicine · 2026Article
- Review
- The Neijiang pig T2T genome reveals domestication history and germplasm traits of Southwest Chinese local breeds.Communications biology · 2026Article
- Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms.Animals : an open access journal from MDPI · 2025Article
- A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research.GigaScience · 2025Article
- FastGA: fast genome alignment.Bioinformatics advances · 2025Article
- Single nucleotide variations in theFrontiers in veterinary science · 2025Article
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Authors and funding
14 authors.
Funding
Abstract
backgroundPigs are crucial sources of meat and protein, valuable animal models, and potential donors for xenotransplantation. However, the existing reference genome for pigs is incomplete, with thousands of segments and centromeres and telomeres missing, which limits our understanding of the important traits in these genomic regions.
findingsWe present a near-complete genome assembly for the Jinhua pig (JH-T2T) and provide a set of diploid Jinhua reference genomes, constructed using PacBio HiFi, ONT long reads, and Hi-C reads. This assembly includes all 18 autosomes and the X and Y sex chromosomes, with only 6 gaps. It features annotations of 46.90% repetitive sequences, 33 telomeres, 17 centromeres, and 23,924 high-confident genes. Compared to the Sscrofa11.1, JH-T2T closes nearly all gaps, extends sequences by 177 Mb, predicts more intact telomeres and centromeres, and gains 799 more genes and loses 114 genes. Moreover, it enhances the mapping rate for both Western and Chinese local pigs, outperforming Sscrofa11.1 as a reference genome. Additionally, this comprehensive genome assembly will facilitate large-scale variant detection.
conclusionsThis study produced a near-gapless assembly of the pig genome and provides a set of haploid Jinhua reference genomes. Our findings represent a significant advance in pig genomics, providing a robust resource that enhances genetic research, breeding programs, and biomedical applications.
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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 Socratic graph.