A comprehensive genomic investigation has produced the first gap-free, telomere-to-telomere reference assembly for the domestic pig,Sus scrofa domesticus, resolving complex chromosomal structures that previously resisted linear reconstruction. The domestic pig serves as a cornerstone of agricultural meat production and functions as an indispensable model organism for human biomedical exploration. An international research consortium initiated sequencing efforts in 2005 using tissue derived from TJ Tabasco, a female Duroc sow. Although the reference was initially published in 2012 and substantially revised in 2017 under the Sscrofa11.1 release, that 2.5-gigabase assembly preserved 93 unresolved gaps. Repetitive satellite blocks and acrocentric centromeres remained largely misassembled or absent, leaving essential regions of the swine genome inaccessible to comparative geneticists.

To overcome these long-standing architectural barriers, researchers combined long-read and ultra-long-read sequencing technologies to assemble the complete chromosome-level resource designated T2T-Sscrofa. Deep sequencing of TJ Tabasco generated 276 gigabases of Pacific Biosciences HiFi long reads exhibiting an average read length of 17,275 base pairs, alongside 395 gigabases of Oxford Nanopore Technologies ultra-long reads with an average length of 91,739 base pairs. Chromosomal architecture was further resolved using 606 gigabases of paired-end 150-base-pair Hi-C chromatin interaction sequencing. The primary assembly, designated T2T-Tabasco, successfully achieved gapless, end-to-end contiguity across all eighteen autosomes and chromosome X. Interaction contact matrices confirmed consistent spatial interactions within and between chromosomal domains, while back-mapping of the HiFi, ultra-long Nanopore, and Hi-C reads covered between 98.81 percent and 99.99 percent of the finished sequence.

Quality assessments demonstrated extraordinary baseline sequence fidelity and structural completeness across the entire reconstructed reference. K-mer spectrum evaluations derived from Pacific Biosciences HiFi data yielded an overall assembly quality value score of 68.8. Rigorous error diagnostics identified potentially erroneous sequences across only 0.4 percent of the genome, while collapsed segments constituted merely 0.2 percent of the final assembly. Minimal overlap was detected between segmental duplications and Flagger-flagged duplicated intervals, measuring 269,147 base pairs or 0.50 percent of all segmental duplications, confirming that these blocks represent genuine genomic loci rather than unmerged haplotype duplications. Because TJ Tabasco is female, researchers incorporated an independent complete Y chromosome sequence from another Duroc male to finalize T2T-Sscrofa. The complete genome encompasses 2,688,404,542 base pairs of nuclear sequence and a 16,740-base-pair mitochondrial genome, achieving a 98.2 percent completeness benchmark in single-copy ortholog assessments.

A critical outcome of the gapless reconstruction is the addition and spatial placement of 274.8 megabases of previously unassembled regions that were missing from Sscrofa11.1. Across individual chromosomes, newly assembled sequences span between 3.8 and 33.3 megabases, displaying overall high collinearity with the predecessor assembly. Systematic decomposition of this added sequence revealed that 140.5 megabases, representing 51.12 percent, correspond to centromeric satellites, while 53.6 megabases represent segmental duplications and 17.1 megabases consist of segmental duplications overlapping centromeres. Additional repetitive elements accounted for 50.7 megabases, and 12.9 megabases comprised unclassified sequences. Overall, identified repetitive elements rose from 45.83 percent in Sscrofa11.1 to 50.24 percent in T2T-Sscrofa, dominated by long interspersed nuclear elements at 26.08 percent, short interspersed nuclear elements at 9.07 percent, and long terminal repeat retrotransposons at 5.07 percent.

Annotation of the complete sequence established an updated inventory of functional genomic units, identifying 21,108 protein-coding genes with a 99.5 percent completeness score under Benchmarking Universal Single-Copy Orthologs evaluation. The pipeline relocated 816 previously unplaced protein-coding genes from disconnected contigs into defined chromosomal coordinates and placed 256 newly annotated protein-coding genes. While non-coding RNA distributions remained broadly comparable to the previous reference, the unbroken assembly enabled the discovery of additional non-coding transcripts within formerly unassembled intervals. Chromosomal termini were confirmed by telomeric sequence arrays identified on every chromosome, exhibiting repeat lengths ranging from 143 base pairs to 1.68 kilobases, verifying the complete linear span of the nuclear pseudomolecules.

The unbroken assembly yielded the first definitive structural resolution of porcine centromeres, establishing clear morphological and sequence divergences between chromosome classes. Autosomes 1 through 12 and chromosome X are metacentric or submetacentric, whereas autosomes 13 through 18 are acrocentric. Pericentromeric satellite repeat arrays on metacentric and submetacentric chromosomes range from 2.5 to 6.5 megabases, dominated by nine specific satellite sequences known as pigcent repeats. In contrast, acrocentric chromosomes harbor massive centromeric arrays ranging from 5.4 to 31.6 megabases, with chromosome 16 containing the largest array at 31.6 megabases. Acrocentric centromeres are dominated by pigcent4, pigcent5, and pigcent6 repeats, displaying elevated repeat density, reduced Hi-C contacts, stable methylation, sparse retrotransposons, and an absence of annotated genes. Unlike human acrocentric short arms, porcine acrocentric short arms lack ribosomal DNA entirely.

Ribosomal DNA arrays represent one of the most recalcitrant assembly challenges in eukaryotic genomics due to their high tandem redundancy. Genomic copy number estimations indicated approximately 214 ribosomal DNA units across the diploid complement. In T2T-Sscrofa, ribosomal DNA arrays map specifically to chromosomes 8, 10, and 14, where chromosome 8 carries tandem 5.8S, 18S, and 28S arrays, chromosome 10 harbors two distinct loci, and chromosome 14 carries isolated 5S repeats. Because bioinformatic copy number estimations exceeded the total physical repeat copies recovered in the linear assembly, researchers cautioned that these complex tandem arrays remain partially unresolved. Nonetheless, the finished genome substantially advances the structural representation of complex repeat regions over all previous iterations.

Leveraging T2T-Sscrofa as an unfragmented reference, the authors investigated structural variation across 45 diverse pigs by mapping long-read sequence datasets with 95.9 to 99.4 percent genome coverage. Variant discovery pipelines identified 46,190 to 60,295 structural variants in European pigs, 81,685 to 84,419 in Tibetan-Berkshire hybrids, and 65,063 to 91,913 in Asian breeds. Merging variant calls generated a unified set of 229,824 high-confidence structural variants, including 126,059 insertions, 101,168 deletions, 1,857 inversions, and 740 duplications. Within previously unassembled regions alone, the catalog captured 27,939 structural variants, predominantly insertions and deletions. Only 2,792 structural variants overlapped gene bodies, whereas 90 percent mapped to non-coding intergenic territory, providing an extensive inventory of previously hidden genomic variation.

To investigate global evolutionary divergence, the researchers analyzed 1,303 whole-genome sequencing samples spanning 156 pig populations at 18.2-fold average depth, retaining 111,457,594 biallelic single-nucleotide polymorphisms and 13,249,688 indels. Population phylogenies split into two primary lineages: Asian domestic and wild pigs, and European domestic and wild pigs. Asian domestic and wild groups maintained higher nucleotide diversity (pi = 0.00352 and 0.00354) than European wild boars (pi = 0.00165), alongside lower linkage disequilibrium and shorter runs of homozygosity. The median fraction of the genome in runs of homozygosity reached 0.206 in Asian domestic pigs compared to 0.415 in European domestic breeds, reflecting centuries of intense artificial selection in Europe. Fixation index scans revealed extreme differentiation in genes regulating morphology and behavior, including MC1R for coat color, TBX19 missense alterations linked to growth and temperament, and EHMT1 missense changes tied to metabolic and adipocyte regulation.

Analysis of chromosome X uncovered a divergent genealogical history marked by four distinct clades and significant lineage-specific haplotype partitioning. A massive 48-megabase low-recombination block on chromosome X displayed two sharply differentiated haplotypes: one widespread across European pigs and northern Asian domestic pigs, and another enriched in southern Asian domestic pigs and Asian wild boars. The southern haplotype shared close genetic affinity with Island Southeast Asian Sus lineages, while northern Asian and European haplotypes clustered separately, indicating ancient introgression from an extinct suid lineage followed by geographic sorting. By establishing a gapless architectural blueprint, T2T-Sscrofa resolves long-standing blind spots in porcine genomics, providing a definitive platform to study mammalian chromosome biology, evolutionary adaptation, and domestic traits.

Subject of Research: Gap-free telomere-to-telomere pig reference genome assembly and Eurasian population diversity

Article Title: A gap-free telomere-to-telomere pig reference genome provides insights into Eurasian pig diversity

Article References: Li, D., Wang, Y., Yuan, T., Li, X., Quan, Y., Tian, X., Liu, W., Schachtschneider, K. M., Schook, L. B., Crooijmans, R. P. M. A., Ding, R., Groenen, M. A. M., Derks, M. F. L., & Yu, T. (2026). A gap-free telomere-to-telomere pig reference genome provides insights into Eurasian pig diversity. Cell Research. https://doi.org/10.1038/s41422-026-01319-4

Image Credits: AI Generated

DOI: 10.1038/s41422-026-01319-4

Keywords: Sus scrofa, pig reference genome, telomere-to-telomere assembly, T2T-Sscrofa, PacBio HiFi, Oxford Nanopore Technologies, Hi-C sequencing, centromeric satellite repeats, acrocentric chromosomes, structural variants, single-nucleotide polymorphisms, runs of homozygosity, Eurasian pig diversity, TBX19 gene, EHMT1 gene, MC1R, X chromosome haplotypes, ribosomal DNA arrays