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Article|10 Aug 2023|OPEN
Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes
Yan Cheng1,2,3 , , Jin Sun1,2,4 , Mengwei Jiang1 , Ziqiang Luo1 , Yu Wang4 , Yanhui Liu1,4 , Weiming Li1 , Bing Hu1,2 , Chunxing Dong1,4 , Kangzhuo Ye1,2 , Zixian Li1,2 and Fang Deng1 , Lulu Wang1 , Ling Cao1,3 , Shijiang Cao5 , Chenglang Pan6 , Ping Zheng1,2 , Sheng Wang3 , Mohammad Aslam1,2 , Hong Wang3 , Yuan Qin,1,2 ,
1State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2Pingtan Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350400, China
3Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
4College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
5College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
6Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad161 (2023)
Views: 89

Received: 01 Feb 2023
Accepted: 30 Jul 2023
Published online: 10 Aug 2023


Soil salinity is a growing concern for global crop production and the sustainable development of humanity. Therefore, it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerance genes to enhance crop tolerance to salt stress. Suaeda glauca, a halophyte species well adapted to the seawater environment, possesses a unique ability to absorb and retain high salt concentrations within its cells, particularly in its leaves, suggesting the presence of a distinct mechanism for salt tolerance. In this study, we performed de novo sequencing of the S. glauca genome. The genome has a size of 1.02 Gb (consisting of two sets of haplotypes) and contains 54 761 annotated genes, including alleles and repeats. Comparative genomic analysis revealed a strong synteny between the genomes of S. glauca and Beta vulgaris. Of the S. glauca genome, 70.56% comprises repeat sequences, with retroelements being the most abundant. Leveraging the allele-aware assembly of the S. glauca genome, we investigated genome-wide allele-specific expression in the analyzed samples. The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression. Moreover, a systematic analysis of the ABCE gene families shed light on the formation of S. glauca’s flower morphology, suggesting that dysfunction of A-class genes is responsible for the absence of petals in S. glauca. Gene family expansion analysis demonstrated significant enrichment of Gene Ontology (GO) terms associated with DNA repair, chromosome stability, DNA demethylation, cation binding, and red/far-red light signaling pathways in the co-expanded gene families of S. glauca and S. aralocaspica, in comparison with glycophytic species within the chenopodium family. Time-course transcriptome analysis under salt treatments revealed detailed responses of S. glauca to salt tolerance, and the enrichment of the transition-upregulated genes in the leaves associated with DNA repair and chromosome stability, lipid biosynthetic process, and isoprenoid metabolic process. Additionally, genome-wide analysis of transcription factors indicated a significant expansion of FAR1 gene family. However, further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S. glauca.