A Haplotype-resolved Telomere-to-Telomere Pig Genome
Zhao, C.; Zhang, Z.; Lin, Z.; Li, J.; Shi, W.; Wu, Y.; Shi, M.; Kong, T.; Wang, B.; Shi, B.; Wang, X.; Xiang, J.; Xu, C.; Fu, Y.; Ming, J.; Qin, Y.; Kuang, J.; Wang, H.; Yao, Y.; Wang, B.; Pei, D.
Show abstract
Haplotype-resolved telomere-to-telomere (T2T) pig genomes have not been reported, but may be essential for xenotransplantation and interspecies chimerism. Here we describe fully phased paternal and maternal T2T assemblies of an Erhualian pig (Ssc_EHL), enabling chromosome-scale reconstruction at base resolution. We uncover 2,498 (paternal haplotype) and 2,577 (maternal haplotype) protein-coding loci previously unresolved in Sscrofa11.1, while maintaining high concordance for anchored gene models between haplotypes. Applying this haplotype-resolved T2T annotation to publicly available pig-to-human kidney xenograft transcriptomes further allows the resolution of xenograft cell states and reveals newly resolved, cell-type-enriched genes. Cross-species synteny and orthology analyses against human identified a subset of high-confidence pig-specific genes with limited human counterparts, thus, refining the genomic basis of interspecies divergence. By integrating these orthology features with organ transcriptomes, we further defined an Interspecies Chimerism Compatibility score to prioritize organ-enriched, highly conserved loci with minimal redundancy imbalance, providing haplotype consistent targets for engineering organ-deficient pigs. Together, this haplotype-resolved T2T pig genome provides a foundational resource for mechanistic studies and rational genome engineering in xenotransplantation and interspecies chimerism.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits 97%
- Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis 97%
- TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function 96%
Similar papers in this journal
- Genomic Insights into the Demographic History and Local Adaptation of Wild Boars Across Eurasia 96%
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon 95%
- Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants 95%
Similar papers in this journal
- Systematic assessment of regulatory effects of human disease variants in pluripotent cells 96%
- Genotyping sequence-resolved copy number variationusing pangenomes reveals paralog-specific global diversityand expression divergence of duplicated genes 95%
- Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish 95%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.