High-quality genome assembly of <i>Carex capillifolia</i> reveals genetic adaptations to drought stress in the Qinghai-Xizang plateau

Yanli Xiong; Qingqing Yu; Yi Xiong; Minghong You; Li He; Guochao Wu; Jinghan Peng; Lijun Yan; Dongzhou Deng; Xiao Ma; Dechao Chen; Daxu Li; Xiong Lei

doi:10.1016/j.jgg.2025.12.011

Volume 53 Issue 5

May 2026

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Article Navigation > Journal of Genetics and Genomics > 2026 > 53(5): 827-840

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High-quality genome assembly of Carex capillifolia reveals genetic adaptations to drought stress in the Qinghai-Xizang plateau

doi: 10.1016/j.jgg.2025.12.011

a. Sichuan Academy of Grassland Sciences, Chengdu, Sichuan 611700, China;
b. College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China;
c. Sichuan Province Forestry and Grassland Key Laboratory of Combating Desertification, Sichuan Academy of Forestry, Chengdu, Sichuan 610081, China;
d. State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China

Funds:

This work was supported by grants from “Tianfu Qingcheng Plan” Science and Technology Innovation Leading Talent Project in 2023, Sichuan Provincial Forestry and Grassland Key Laboratory of Combating Desertification (KJZXSA202310), Sichuan Province “14th Five-Year Plan” Forage Breeding Research Project (2021YFYZ0013-2), the National Modern Forages Industry Technology System (CARS-34), and Sichuan Forage Innovation Team Program (SCCXTD-2020-16).

Received Date: 2025-04-23
Accepted Date: 2025-12-24
Rev Recd Date: 2025-12-23

Available Online: 2026-05-15

Publish Date: 2026-05-30

Abstract

Abstract

Carex capillifolia is an ecologically and economically important fodder grass widely distributed across the Northern Hemisphere, particularly in the Qinghai-Xizang Plateau. Research into its genetic diversity and genomic architecture has been limited. In this study, we present a high-quality genome assembly for C. capillifolia, spanning 386.65 Mb (contig N50 = 14.66 Mb) and comprising 29 chromosomes. Phylogenetic analysis reveals a close evolutionary relationship with C. littledalei, with divergence estimated at 2.19–6.1 million years ago. Comparative genomics analyses identify 26 shared chromosome fusion events specifically between these two species, highlighting a pattern of recent, lineage-specific karyotype reshuffling that contributes to the remarkable karyotypic diversity within Cyperaceae. Using population genomics, genome-environment association (GEA), and transcriptome analysis, we identify multiple climate-associated genetic variants and drought-tolerance genes. Notably, we identify an auxin response factor (ARF) gene and verify its role in enhancing drought tolerance through transgenic experiments. Furthermore, we pinpoint the Ruoergai (RRG) geo-group as possessing the highest adaptability to future climates, which harbors superior adaptive genetic variation and candidate genes that could be targeted in breeding closely related species.
- Genome,
- Population genomics,
- Carex capillifolia,
- Environmental adaptation

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