Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes

Abstract

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.

Acknowledgements

We thank Chunyin Zhang for providing the original seeds of S. glauca. We also thank the editors and reviewers for their valuable feedback on this manuscript. This work was supported by the National Natural Science Foundation of China (32170380), the Science and Technology Innovation Project of Pingtan Institute of Science and Technology (PT2021001), and the Postdoctoral Foundation of China (2018 M642550).

Author contributions

Y.C. and Y.Q. conceived and designed the research. J.S. and M.J. conducted genome assembly and annotation. J.S., Y.L., W.L., and P.Z. conducted other bioinformatic work. B.H., C.D., K.Y., Z.Li., F.D., L.W., and L.C. performed laboratory experiments. H.W., M.A., S.W., S.C., C.P., and Y.Q. contributed to critical discussions on the work. Z.Luo. wrote a draft of the introduction, M.J. wrote the materials and methods section, and Y.C. wrote the other sections and was responsible for writing. M.A. and Y.Q. revised the manuscript. All authors discussed the results, contributed to manuscript preparation, and approved the final version of the manuscript.

Data availability

All relevant data are contained within the article or supplementary materials.

Conflict of interest

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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