Abstract
The reed vole (Microtus fortis) is an important rodent model for studying unique biological traits, such as its natural resistance to Schistosoma japonicum. To facilitate the genetic study of these phenotypes, we have produced the first high-quality, chromosome-level genome assembly for this species. The genome was assembled using PacBio HiFi long-read sequencing and scaffolded to the chromosome level with Hi-C data. The final 2.29 Gb assembly exhibits excellent continuity (contig N50 = 68.89 Mb; scaffold N50 = 91.23 Mb), with 97.7% of the sequence anchored into 26 pseudomolecules, consistent with the species’ karyotype. Genome completeness was estimated at 96.3% via BUSCO analysis (glires_odb10). The annotation includes 23,678 protein-coding genes, with 97.5% assigned a putative function. This publicly available, high-quality genomic resource will be invaluable for future research, providing the necessary foundation to explore the genetic mechanisms behind the unique adaptations of M. fortis, including its innate immunity, digestive physiology, and disease models. The assembly will also serve as a key reference for comparative genomics, enriching our understanding of rodent evolution.
Data availability
The raw sequencing data (including Illumina, PacBio HiFi, Hi-C, and transcriptomic reads) generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under study accession number SRP58974844. The complete mitochondrial genome is available in GenBank under accession number PX549189.150. The final chromosome-level genome assembly and annotation have been deposited in GenBank under accession number JBQVRV000000000.151 and in the Genome Warehouse (GWH) at the National Genomics Data Center (NGDC) under accession number GWHESEF0000000052. All data are associated with BioProject accession number PRJNA1271721.
Code availability
No custom code was generated for this study. All analyses were performed using publicly available bioinformatics tools as described in the methods section.
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Acknowledgements
This work was supported by the Changsha Major Special Project of Science and Technology (Grant No. kh2301027), the Natural Science Foundation of Hunan Province (Grant Nos. 2024JJ5422 and 2024JJ6494), and the Key Research and Development Program of Hunan Province (Grant No. 2024DK2001). The authors are grateful to Benagen Technology (Wuhan, China) for their valuable advice on bioinformatic analysis. We also sincerely thank the journal editors and the reviewers for their constructive suggestions and insightful comments, which significantly contributed to the improvement of this manuscript.
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Z.J.Z. and Q.H. conceived and designed the study; T.Q.H. and J.K.Z. conducted the collection of the reed vole samples; J.K.Z., Y.X.W., Q.L., J.Z., W.L.Z., L.X.O., S.S.G., R.T.G. contributed to experimental design and data collection. D.Z. analyzed the data and wrote the draft manuscript; D.Z., T.Q.H., Q.H. and Z.J.Z. discussed the results and improved and revised the manuscript. All authors reviewed the manuscript.
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Zhang, D., Hu, Q., He, T. et al. Assembling a chromosome-level genome for the Microtus fortis using PacBio HiFi and Hi-C technologies. Sci Data (2026). https://doi.org/10.1038/s41597-026-06813-3
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DOI: https://doi.org/10.1038/s41597-026-06813-3
