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Telomere-to-Telomere genome assembly of an endangered tree Berchemiella wilsonii (Rhamnaceae)

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Abstract

Berchemiella wilsonii (Schneid.) Nakai is one of the National Key Protected Wild Plants in China, and one of the 120 Plant Species with Extremely Small Populations in China. By combining PacBio HiFi sequencing, DNBSEQ sequencing and Hi-C sequencing, we have assembled a chromosome-scale, haplotype-resolved genome for B. wilsonii. The final assembled haplotype A and haplotype B genomes were 216.84 Mb and 217.69 Mb, anchored to 2n = 24 chromosomes, all chromosomal ends contain telomeric characteristic motifs (TTTAGGG), only haplotype A has one gap, both close to a T2T genome assembly, with contig N50 lengths of 18.24 Mb and 18.03 Mb, respectively. Further, BUSCO analysis showed an extremely high assembly completeness (98.9% complete BUSCO genes). The genome contains a total of 22,828 coding genes, of which 21,992 (96.34%) were functionally annotated. This is the first report of the genome of B. wilsonii and the high-quality genome will provide new insights into evolutionary history and taxonomic classification challenges of endangered plant species.

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Data availability

The raw date of PacBio HiFi, DNBSEQ and Hi-C sequencing data generated in this study have been deposited at the NCBI Sequence Read Archive (SRA) under the BioProject number of PRJNA1229120. The accession numbers of PacBio HiFi, DNBSEQ and Hi-C sequencing data are publicly accessible as SRR3577978367, SRR3577978568, and SRR3577978469, respectively. Furthermore, the raw data were also deposited at the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) with accession number CRA02411470 under BioProject accession numbers PRJCA037665. RNA-seq data for root, stem, and leaf tissues have been deposited at the NCBI Sequence Read Archive (SRA) under accessions SRR3278399471, SRR3276777072, and SRR3278399373, respectively. The final genome assembly has been deposited in NCBI GenBank with accession number JBMIOF00000000074 and JBMIOG00000000075 for haplotype A and haplotype B, respectively. The annotation files of the genome are available at the Figshare database76.

Code availability

We did not use any custom code in this study. The versions and parameters of the bioinformatic tools used in this study were described in the Methods section. If a parameter was used with other than its default value, this was stated above as well.

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Acknowledgements

This work was financially supported by National Natural Science Foundation of China (U2571202; 32371653) and National Key R&D Program of China (2024YFF1307400).

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Author notes

  1. These authors contributed equally: Jianghao Pang, Zhiqiang Xiao.

Authors and Affiliations

  1. State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China

    Jianghao Pang, Shuaishuai Song, Hao Wu, Xinzeng Wei & Mingxi Jiang

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Jianghao Pang, Shuaishuai Song, Hao Wu, Xinzeng Wei & Mingxi Jiang

  3. China Three Gorges Corporation, Wuhan, 430010, China

    Zhiqiang Xiao

  4. Hubei Wufeng Houhe National Nature Reserve Administration, Wufeng, 443400, Hubei, China

    Yeqing Wang & Yufen Cheng

  5. Jixi Management Station of Anhui Qingliangfeng National Nature Reserve, Xuancheng, 245300, Anhui, China

    Yunlong Tang

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  1. Jianghao Pang
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Contributions

X.W. and M.J. conceived and supervised the study. J.P., Z.X., Y.W., Y.C., S.S., H.W. and X.W. performed the experiments and analysed the data. J.P. and X.W. wrote the draft of the manuscript. All authors reviewed and contributed to the final version of the manuscript.

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Xinzeng Wei.

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Pang, J., Xiao, Z., Wang, Y. et al. Telomere-to-Telomere genome assembly of an endangered tree Berchemiella wilsonii (Rhamnaceae).
Sci Data (2025). https://doi.org/10.1038/s41597-025-06433-3

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