SinoXivDiploid telomere-to-telomere assemblies reveal hierarchical satellite architectures and heritable MHC structural diversity in macaques
Abstract
The crab-eating macaque (Macaca fascicularis), a key biomedical model, exhibits substantial inter-individual variability. However, its genomic architecture remains incompletely resolved due to extensive structural complexity and reliance on haploid reference assemblies. Here, we generated 24 diploid telomere-to-telomere (T2T) haplotypes from 12 male and female individuals representing three geographic populations including a pedigree, enabling systematic interrogation of genome architecture at diploid resolution with geographic diversity and familial inheritance. We identified previously uncharacterized large inter-chromosomal repeat clusters with haplotype-specific organization that are conserved among old world monkeys. In addition, twenty-four completely contiguous major histocompatibility complex (MHC) haplotypes reveal extensive inter or intra individual variations in gene copy number and structural organization of the class-IA, IB, and II regions. Together, these findings demonstrate that diploid T2T assemblies are essential for accurately capturing structural and immunogenetic diversity in non-human primates and provide a genomic framework for precision immunogenomics in this widely used biomedical model.
Citation Information
@article{seiyaimoto2026,
title={Diploid telomere-to-telomere assemblies reveal hierarchical satellite architectures and heritable MHC structural diversity in macaques},
author={Seiya Imoto and Takuya Yamamoto and Yusuke Nakamura and Shokichi Takahama and Kazuma Kiyotani and Toyomasa Katagiri and Emiko Urano and Nobuhiro Shimozawa and Naohide Ageyama and Yasuhiro Yasutomi and Kotoe Katayama and Yoshimasa Ono and Noriaki Sato and Takayoshi Hyugaji and Hiroko Tanaka and Takanori Hasegawa and Satoru Miyano and Nicholas Ong and Lin Yang and Miles Benton and Lihye Kim and Ratna Sariyatun and Yuta Nagatsuka and Takuto Nogimori},
journal={Research Square},
year={2026},
doi={https://doi.org/10.21203/rs.3.rs-9105354/v1}
}
