Abstract
The Siberian crane (Leucogeranus leucogeranus) is classified as Critically Endangered by the IUCN. Its current estimated population is over 6,900 individuals in East Asia, whereas the Western/Central Asian population is nearly extinct, with no recent records of its presence in the wild. Here, we present a high-quality, chromosome-level genome assembly of the Siberian crane generated by integrating Nanopore long-read data, MGISEQ-2000 short-read data, and Hi-C technology data. The assembled genome spans 1.31 Gb, with a scaffold N50 of 83.45 Mb, comprising 33 chromosomes and additional unplaced scaffolds. BUSCO assessment indicated that 97.3 percent of genes in the genome assembly are complete. We identified 10.9 percent repetitive sequences and 21,678 protein-coding genes, of which 88 percent were successfully assigned functional annotations. This high-quality genome assembly and annotation provide a valuable genomic resource for comparative genomic research aimed at understanding the ecology, evolutionary adaptations, and development of Gruidae birds.
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Data availability
The Hi-C data described in this study are available at in the NCBI Sequence Read Archive database with accession number SRR35316027 (https://www.ncbi.nlm.nih.gov/sra/SRP618574). The sequencing data obtained from the MGISEQ-2000 platforms are deposited into NCBI Sequence Read Archive database with accession number SRR35316036-42 (https://www.ncbi.nlm.nih.gov/sra/SRP618574). The genome assembly is deposited into the DDBJ/ENA/GenBank with accession number JBQWBR000000000 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_053455625.1). The annotation files are available from Figshare (https://doi.org/10.6084/m9.figshare.30017956). All data are publicly available and includes raw sequencing reads, assembled genome, genome annotation files, functional annotation results. Metadata describing the sample information, sequencing platforms, and assembly statistics are also provided in the same repository.
Code availability
The assembly and annotation were performed following the manuals of the corresponding bioinformatics tools with default parameters. The code of the quality assessment and result visualization is available at https://github.com/ChenqCQ/Siberian_crane_Chromosome.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (32160132, 32471732) and the Forestry Administration of Guangdong Province, China (DFGP Project of Fauna of Guangdong-202115; Science and Technology Planning Projects of Guangdong Province-2021B1212110002). We appreciate the technical support from the Beijing Genomics Institute (BGI) and EasyATCG Science and Technology Company for sequencing, assembly, and annotation. We appreciate Dr. Russell Doughty for his substantial contributions to improving the readability of this manuscript.
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Yang Liu and Wenjuan Wang conceived and designed the experiments. Peng Huang, Nianhua Dai, and Marria Vladimirtseva collected the samples. Qing Chen performed quality assessment and analyzed the data. Qing Chen wrote the manuscript. Chenqing Zheng, Yang Liu, and Wenjuan Wang reviewed the manuscript.
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Chen, Q., Zheng, C., Huang, P. et al. Chromosome-level genome assembly and annotation of the critically endangered Siberian crane (Leucogeranus leucogeranus). Sci Data (2026). https://doi.org/10.1038/s41597-026-06773-8
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DOI: https://doi.org/10.1038/s41597-026-06773-8
