Abstract
The Yarkand hare (Lepus yarkandensis) is endemic to the Tarim Basin in Xinjiang, China. It is a key species and a critical component of the Tarim Basin ecosystems. However, the lack of a reference genome has hindered evolutionary and genetic studies of this species. Here, we assembled a telomere-to-telomere (T2T) genome of the Yarkand hare (LepYark_1.0) using PacBio HiFi, Nanopore, and Hi-C sequencing. The assembled genome size is approximately 2.70 Gb, with a scaffold N50 of 126.86 Mb. About 94.88% of the assembled sequences could be anchored to 24 pseudo-chromosomes, with a BUSCO assessment indicating a completeness of 99.0%. Repetitive sequences comprise 46.38% of the genome, with short interspersed nuclear elements (SINEs) accounting for the largest proportion. Additionally, we identified 24 centromeres and 46 telomeres. 32,298 protein-coding genes were annotated using de novo prediction and transcriptome data, functionally annotating 85% of them. This genome assembly provides genomic resources for studies on conservation, adaptive evolution and the exploration of genetic basis related to important traits of the Yarkand hare.
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Data availability
The assembled genome data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.gca:GCA_047496845.153.
The annotation data that support the findings of this study are openly available in figshare at https://doi.org/10.6084/m9.figshare.29369999.v154.
The Illumina sequencing data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.sra:SRR3690616455.
The PacBio sequencing data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.sra:SRR3690616855.
The Nanopore sequencing data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.sra:SRR3690616655, https://identifiers.org/ncbi/insdc.sra:SRR3690616755.
The Hi-C sequencing data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.sra:SRR3690616955.
The RNA sequencing data that support the findings of this study are openly available in NCBI at https://identifiers.org/ncbi/insdc.sra:SRR3690616555.
Code availability
All software used in this work is in the public domain, with parameters being clearly described in Methods. If no detail parameters were mentioned for a software, default parameters were used as suggested by developer.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (32260116) and the Central Guidance for Local Projects of Xinjiang (ZYYD2024ZY04). Thanks to Associate Professor Linqiang Zhong of Xinjiang University for providing the photo of the Yarkand hare (Fig. 1a) and assisting in the sample collection.
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In this study, Mengqi Xu was responsible for data collation and paper writing, Yuge Cui and Hongcheng Kuang were responsible for sample collection and collation, Kai Wei was responsible for technical guidance and paper revision, and Wenjuan Shan was responsible for outline writing, project management, and funding acquisition.
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Xu, M., Cui, Y., Kuang, H. et al. Telomere to telomere level genome assembly of the Yarkand hare (Lepus yarkandensis). Sci Data (2026). https://doi.org/10.1038/s41597-026-06815-1
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DOI: https://doi.org/10.1038/s41597-026-06815-1
