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Chromosomal-level genome assembly of two dominant desert shrub species in Haloxylon (Amaranthaceae)

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Abstract

Haloxylon ammodendron and Haloxylon persicum are ecologically and economically important drought-tolerant plants, often referred to as “desert guardians” owing to their remarkable abilities to withstand conditions of drought and salinity. We conducted a chromosome-level genome assembly using PacBio HiFi long-read sequences and Hi-C technology in order to gain a deeper understanding of their adaptive mechanisms and resource potential. The final assembled genome sizes were 2.32 Gb (contig N50 = 5.11 Mb; Scaffolds N50 = 257.59 Mb) for H. ammodendron and 1.32 Gb (contig N50 = 9.55 Mb; Scaffolds N50 = 143.67 Mb) for H. persicum, with 97.84% and 95.45% of the respective sequences anchored to nine pseudochromosomes. The BUSCO integrity scores were 88.40% and 84.00% for H. ammodendron and H. persicum, respectively. Gene annotation revealed that H. ammodendron contained 69,844 protein-coding genes, while H. persicum had 66,859 protein-coding genes, with repeat elements constituting 57.42% and 52.88% of their genomes, respectively. The reference genomes of Haloxylon serve as invaluable resources for exploring the ecological and economic significance of desert plants.

Data availability

All raw sequencing data can be obtained from NCBI genome database, the genome annotation files can be accessed from the Figshare databases.

Code availability

All software involved in this research analysis was implemented according to the manuals and protocols provided by the software developers. The software versions were listed in the methods. Custom code was not used in this study.

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Acknowledgements

We thank the associate editor and anonymous reviewers for their helpful comments. This work was supported by the Central Government Guide Local Special Fund Projects for Science and Technology Development (ZYYD2025ZY04), the National Natural Science Foundation of China (Youth Fund) (32301307), and the Natural Science Foundation of Xinjiang Uygur Autonomous Region (2023D01C186). We thank LetPub (www.letpub.com.cn) for linguistic assistance and pre-submission expert review.

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Authors and Affiliations

  1. School of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, 830017, China

    Fang Yang, Di Gao, Yifei Wang, Xuelian Ding & Guanghui Lv

  2. Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi, 830017, China

    Fang Yang, Di Gao, Yifei Wang, Xuelian Ding & Guanghui Lv

  3. Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, 833300, China

    Fang Yang, Di Gao, Yifei Wang, Xuelian Ding & Guanghui Lv

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  1. Fang Yang
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  5. Guanghui Lv
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Contributions

F.Y. conceived the study; F.Y. collected data, analyzed the data, and drafted the text; D.G. collected and analyzed the data; Y.F.W. and X.L.D. collected samples; G.L. revised the manuscript. All of the authors edited the manuscript.

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Correspondence to
Guanghui Lv.

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Yang, F., Gao, D., Wang, Y. et al. Chromosomal-level genome assembly of two dominant desert shrub species in Haloxylon (Amaranthaceae).
Sci Data (2025). https://doi.org/10.1038/s41597-025-06514-3

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