Genome assembly and annotation of the naked mole rat Heterocephalus glaber reared in Japan

2025 · doi:10.1101/2025.05.20.654782
preprint OA: closed CC-BY-NC-ND-4.0
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This paper generated a new genome assembly for the naked mole rat (Heterocephalus glaber) using PacBio long-read sequencing from animals reared in Japan, aiming to clarify the role of intraspecific genomic variation. The authors assembled a 2.56 Gb genome with 95.2% BUSCO completeness and predicted 26,714 protein-coding genes, adding functional annotations for 26,232 genes via a BRAKER3-based workflow. They further identified 417 gene models not detected in the earlier reference genome and reported structural and amino acid sequence differences between this assembly and the reference, interpreted as intraspecific variation. The study’s major limitation is that it focuses on building and benchmarking the genomic resource rather than directly testing functional consequences of the detected variants. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

The naked mole rat (NMR, Heterocephalus glaber ) is a eusocial rodent that is native to northeastern Africa. NMRs exhibit extraordinary traits such as longevity, resistance to age-related decline, and remarkable hypoxia tolerance. Although the reference genome of this species has been determined because of its unique characteristics, the significance or role of intraspecific genomic variations remains unknown. In this study, we used PacBio long-read sequencing to generate a genome assembly of NMR reared in Japan. The assembled genome is 2.56 Gb. Benchmarking Universal Single–Copy Orthologs (BUSCO) revealed high completeness (95.2%). BRAKER3 estimated 26,714 protein-coding genes, and we successfully added functional annotations for 26,232 protein-coding genes using the functional annotation workflow. We identified 417 gene models that were previously undetectable in the reference genome of this species. We also identified structural and amino acid sequence variations between our assembly and the reference genome, suggesting the presence of intraspecific genomic variations. This new genomic resource could help uncover the molecular mechanisms underlying the behavioral and physiological traits of NMR.
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Abstract The naked mole rat (NMR, Heterocephalus glaber) is a eusocial rodent that is native to northeastern Africa. NMRs exhibit extraordinary traits such as longevity, resistance to age-related decline, and remarkable hypoxia tolerance. Although the reference genome of this species has been determined because of its unique characteristics, the significance or role of intraspecific genomic variations remains unknown. In this study, we used PacBio long-read sequencing to generate a genome assembly of NMR reared in Japan. The assembled genome is 2.56 Gb. Benchmarking Universal Single–Copy Orthologs (BUSCO) revealed high completeness (95.2%). BRAKER3 estimated 26,714 protein-coding genes, and we successfully added functional annotations for 26,232 protein-coding genes using the functional annotation workflow. We identified 417 gene models that were previously undetectable in the reference genome of this species. We also identified structural and amino acid sequence variations between our assembly and the reference genome, suggesting the presence of intraspecific genomic variations. This new genomic resource could help uncover the molecular mechanisms underlying the behavioral and physiological traits of NMR. Competing Interest Statement The authors have declared no competing interest.

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License: CC-BY-NC-ND-4.0