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Integrated metatranscriptome and transcriptome reveals the microbial community composition and physiological function of xylem sap on grapevine during bleeding period

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Abstract

Background

The xylem sap of fruit trees ensures the survival during the dormant period, and its flow during the bleeding period is correlated with the start of a new life cycle. Though the simple exploration on ingredients in the sap was carried out in the early years, the specific life activities and physiology functions of the sap during bleeding period have not been reported yet and the bleeding period is still a fruit tree development period worthy of attention.

Objectives

In this study, the microbial community composition during bleeding period were revealed by metatranscriptome and transcriptomic data. For the first time, the microorganism genome and grape genome in xylem sap were analyzed on transcriptional level, based on which the main physiological functions of the sap were also determined.

Methods

The genomic RNA in the sap was isolated and sequenced. Kyoto Encyclopedia of Gene and Genome (KEGG), Evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Carbohydrate-Active enzymes Database (CAZy) functional annotation were used to analysis the function of micro-organisms in xylem sap. DEGs were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The genes responsive to biotic and abiotic stresses were finally screened by transcriptome screening, stress data analysis and vitro validation experiments.

Results

The analysis exhibited 36,144,564 micro-related clean reads and 244,213 unigene. KEGG, eggNOG and CAZy functional annotation analysis indicated that signal transduction and material metabolism were the most important function of xylem sap. DEGs analysis were mainly about disease resistance, carbon source metabolism and hormone signal transduction, especially in P3 vs P1, enriched in the plant-pathogen interaction pathway. Analysis on grape genome information revealed xylem sap had little RNA with weak life activity. Metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction and plant-pathogen interaction were the four pathways with the largest number of enriched genes. Moreover, 16 genes responsive to biotic and abiotic stresses were screened out.

Conclusion

Promoting plant growth and resisting pathogens were the most important function of xylem sap during the bleeding period, and the function of microbial community were closely related to microorganisms growth and disease resistance. The 16 stress-related genes might be used for the future grape resistance research.

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Acknowledgements

This research was supported by Project Funded by the Natural Science Foundation of China (NSFC) (No. 31672131), Jiangsu Sanxin Engineering Project (SXGC [2017]278) and Jiangsu major species creation Project (PZCZ201724).

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Authors and Affiliations

  1. College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, Jiangsu, China

    Zheng Ting, Zhang Kekun, Zhu Xudong, Guan Le, Li Xiaopeng, Mazzullah Nasim, Jia Haifeng & Fang Jinggui

  2. Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200030, People’s Republic of China

    Jiu Songtao

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  1. Zheng Ting
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  2. Zhang Kekun
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  3. Zhu Xudong
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  6. Li Xiaopeng
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Correspondence to Fang Jinggui.

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Zheng, T., Zhang, K., Zhu, X. et al. Integrated metatranscriptome and transcriptome reveals the microbial community composition and physiological function of xylem sap on grapevine during bleeding period. Genes Genom 41, 1095–1111 (2019). https://doi.org/10.1007/s13258-019-00841-7

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