A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic

Abstract

The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by the accumulation of viruses. Herein, we describe a single-cell transcriptomic atlas of swelling cloves with virus accumulation, which comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells of two clusters, clusters 7 (C7) and 11 (C11), were inferred to be from the meristem. Cell trajectory analysis suggested the differentiation of clove cells to start from the meristem cells, along two pseudo-time paths. Investigation into the cell-specific activity of invasive viruses demonstrated that garlic virus genes showed relatively low-expression activity in cells of the clove meristem. There were 2060 garlic genes co-expressed with virus genes, many of which showed an association with the defense response. Five glutathione synthase/reductase genes co-expressed with virus genes displayed up-regulated expression, and the glutathione and related metabolites level showed an alteration in virus-invasive garlic clove, implying the role of glutathione in viral immunity of garlic. Our study offers valuable insights into the clove organogenesis and interaction between garlic and virus at single-cell resolution.

Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (32372689), Shandong Provincial Key Research and Development Program (2023CXPT045), Shandong Provincial Technological Innovation Capability Enhancement Project of Small and Medium-Sized Enterprises (2023TSGC0315), Jining Key Research and Development Program (2022HHCG017), Jiangsu Provincial Basic Research Program of Higher Education (23KJB210017).

Author contributions

S.G., F.L., and Z.Z. contributed equally to this work. S.G. performed the scRNA-seq. F.L. and Z.Z. performed the experiment. S.Z. conducted data analyses. Q.H. monitored the growing state of cloves, collected samples, and took photographs. Y.W. and T.W. carried out the field experiment and trait investigation. H.M. revised the manuscript. T.L. designed the analyses and wrote the manuscript.

Data availability statement

The raw scRNA-seq data reported in this paper have been deposited in the Genome Sequence Archive [68] in the National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA011872). The sequence reads of transcriptome and the expression data have been deposited in the NCBI GEO database under the accession number GSE185962.

Conflict of interests

The authors have no competing interest to declare.

Supplementary data

Supplementary data is available at Horticulture Research online.

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