Single-nucleus transcriptomics reveals the cellular immune responses to Candidatus Liberibacter asiaticus in rough lemon

Abstract

Citrus Huanglongbing (HLB) is the most destructive disease in citriculture, mainly caused by Candidatus Liberibacter asiaticus (CLas). However, the immune response of citrus to CLas at the cellular level remains to be elucidated. In this study, the first single-cell atlas of rough lemon (Citrus jambhiri Lush.) root apexes were generated using single-nucleus RNA sequencing at 20 weeks postinoculation with CLas. According to gene expression patterns, the single-cell atlas was partitioned into 20 transcriptionally distinct clusters, and five cell types were identified within these clusters. A significant number of defense-related genes were co-upregulated across the five cell types following CLas infection, whereas genes involved in signal transduction pathways, such as tubulin beta-6 chain (TUBB1) and the phospholipase D alpha 1 (PLD1), were concurrently downregulated. Based on pseudotime trajectory analysis, the key pathways and genes involved in the coordination of cell differentiation and resistance in citrus under CLas infection were characterized. Following CLas infection, the development of phloem cells was significantly delayed, and the differentiation of cambium cells into xylem cells was evident. The expression of genes associated with lignin synthesis was significantly upregulated in these cells. The reduction in phloem cell differentiation and the enhanced differentiation of cambium cells into defense-related xylem cells may represent the primary vascular immune mechanisms exhibited by citrus plants in response to CLas infection. Additionally, DNA-binding one zinc finger transcription factor DOF2.4 was found to potentially serve dual roles in regulating vascular cell development and inducing plant resistance against CLas. In conclusion, this study collectively provides insights into the cellular innate immunity responses of citrus to CLas infection. These findings hold significant implications for the sustainable development of citriculture amidst the ongoing global HLB epidemic, and offer novel insights into vascular immunity and plant defense responses.

Acknowledgements

This study was supported by the Rural Revitalization Project of Chinese Academy of Sciences (KCXFZJ-DDBF-202403), the Innovation Research 2035 Pilot Plan of Southwest University, China Agriculture Research System (CARS-26-05B), and the National Key R&D Program of China (Grant no. 2021YFD1400800).

Authors contributions

Conceptualization, X.B.T. and Z.S.; methodology, X.B.T., J.Z., J.L. and Y.L.; software, X.B.T.; validation, X.B.T. and Z.S.; formal analysis, X.B.T. and Z.S.; investigation, X.B.T. and Z.S.; writing—original draft preparation, X.B.T.; writing—review and editing, X.B.T., C.Z. and Z.S.; funding acquisition, C.Z. and Z.S. All authors have read and agreed to the published version of the manuscript.

Data availability

The snRNA-seq data have been deposited in National Genomics Date Center under accession number PRJCA047249.

Conflicts of interest statement

The authors confirm that they have no conflicts of interest concerning this research.

Supplementary material

Supplementary material is available at Horticulture Research online.

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