Sequencing & Pangenomes
Authors: Leland Ackerson (Michigan State University) , Temitayo Olagunju (University of Idaho) , Mehak Kapoor (Iowa State University) , Arthur Durante (Université de Toulouse) , Morgan R. Stegemiller (University of Idaho) , Katie Shira (University of Idaho) , Kristen Kuhn (USDA) , Lel Eory (The University of Edinburgh) , Wen Huang (Michigan State University) , Brenda Murdoch (University of Idaho) , Alan Archibald (The University of Edinburgh) , Timothy P. L. Smith (USDA) , Christopher Tuggle (Iowa State University) , Ben Rosen (USDA) , Emily Clark (European Bioinformatics Institute)
Genomics applications require a high-quality reference genome to serve as a standard reference map. The current Sus scrofa reference genome contains a large number of unresolved gaps of unknown and unplaced sequences, the vast majority of which are derived from repetitive regions. Advances in long-read sequencing overcomes the challenges in resolving repetitive sequences and has the potential to generate complete, gapless, telomere-to-telomere (T2T) genome assemblies. Here we report the generation of two haplotype resolved T2T genome assemblies. We employed a trio-based approach, sequencing a F1 male with PacBio HiFi and ONT Ultra-Long technologies and the Hampshire sire and the Yorkshire and Landrace composite dam with Illumina short-read technology. Additionally, we generated Omni-C data to aid haplotype resolution. The parental haplotypes for the F1 individual were assembled using Verkko, followed by manual correction and detangling based on coverage, haplotype-markers, and read alignments. The curated and detangled assemblies were then polished with short-read sequences to improve base calling accuracy. The final assembly has telomeres placed on every chromosome (n=19), with the sire haplotype (Hampshire) having 16 T2T contigs (Chrs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 , 11, 12, 13, 17, 18, and Y) and 3 T2T scaffolds (Chrs: 14, 15, and 16), and the dam haplotype (Yorkshire x Landrace) having 17 T2T contigs (Chrs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, and X ) and 2 T2T scaffolds (Chrs: 15 and 16). Ribosomal DNA (rDNA) arrays were resolved with copy number estimated. The mitochondrial genome is also assembled and circularized. The assembly offers significant improvements in terms of contiguity and completeness relative to the current reference genome (Sscrofa11.1; N50=48.2Mb). Each haplotype has QV > 56, N50 > 145 Mb, and a 98.5% diploid BUSCO score. Over 120 Mb and 106 Mb of novel sequences were identified relative to the current reference genome in the Hampshire and Yorkshire x Landrace haplotypes, respectively. Additional work is ongoing to annotate these genomes using functional genomics data including CENP-A ChIP-Seq, RNA-Seq, ATAC-Seq, Iso-Seq, and single-nuclei RNA-Seq. These T2T genomes will be immensely useful for genomics applications including comparative genomics, reference-based mapping, and pangenomics. The availability of these reference genomes will enable studies of genome function and genetic variation, and enhance our understanding of porcine biology - contributing to the genetic improvement of the pig.
Keywords: 2026
How to Cite: Ackerson, L. , Olagunju, T. , Kapoor, M. , Durante, A. , Stegemiller, M. R. , Shira, K. , Kuhn, K. , Eory, L. , Huang, W. , Murdoch, B. , Archibald, A. , Smith, T. , Tuggle, C. , Rosen, B. & Clark, E. (2026) “T2T genomes for the pig”, World Congress on Genetics Applied to Livestock Production Digital Archive. 2026(1). doi: https://doi.org/10.31274/wcgalp.23812