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Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress

  • Lingfei Shangguan
  • Xiang Fang
  • Lide Chen
  • Liwen Cui
  • Jinggui Fang
Original Article


Main conclusion

Grapevine autophagy-related genes (ARGs) include 35 members that have unique evolutionary backgrounds and expression patterns, with some of them responding to abiotic stresses, including copper stress.

Autophagy is one of the most crucial self-regulating phenomena in livings organisms, including animals, plants, yeasts, etc. In the genomes of plants, like Arabidopsis, rice, tobacco, and barley, more than 30 autophagy-related genes (ARGs) have been found. These ARGs are involved in plant development, programed cell death, and the stress response process. In plants, and particularly in grapevine, high copper stress results from the application of the Bordeaux mixture, a widely used fungicide. However, the function of autophagy in plant tolerance to copper stress is unknown. Accordingly, in this study, a genome-wide analysis was performed to identify Vitis vinifera ARGs (VvARGs), and 35 VvARGs were detected. A gene family analysis revealed that the tandem and segmental duplication events played significant roles in the VvARG gene family expansion. Moreover, there was more intense signature of purifying selection for the comparison between grape and rice than between grape and Arabidopsis. In response to copper treatment, both the autophagosome number and malondialdehyde concentration increased during the initial 4 h post-treatment, and reached maximal values at 24 h. An expression analysis indicated that most VvARGs responded to copper stress at 4 h post-treatment, and some VvARGs (e.g., VvATG6, VvATG8i, and VvATG18h) exhibited responses to most abiotic stresses. These results provide a detailed overview of the ARGs in grapevine and indicate multiple functions of autophagy in fruit development and abiotic stresses in grapevine. The key ARG (e.g., ATG8i) should be investigated in more detail in grapevine and other plant species.


Grapevine Autophagy Copper stress VvARGs Autophagosome 



Autophagy-related genes




Methyl viologen


Oxidative species


Superoxide dismutase








Non-synonymous substitutions per non-synonymous site


Synonymous substitutions per synonymous site


Reads per kilobase per million mapped reads






Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

425_2018_2864_MOESM1_ESM.xlsx (63 kb)
Supplementary material 1 Table S1 Summary of target genes used in this study. Table S2 Detailed information for grapevine autophagy-related genes. Table S3 Detailed information for rice autophagy-related genes. Table S4 Detailed information for Arabidopsis autophagy-related genes. Table S5 Detailed information for tobacco autophagy-related genes. Table S6 Ka/Ks analysis of duplicated VvARG and AtARG homologues. Table S7 Ka/Ks analysis of duplicated VvARG and OsARG homologues (XLSX 63 kb)
425_2018_2864_MOESM2_ESM.docx (6.5 mb)
Supplementary material 2 Figure 1. Protein alignment of the autophagy-related genes families. (a). Protein alignment of the ATG1 family; (b). Protein alignment of the ATG13 family; (c). Protein alignment of the ATG18 family; (d). Protein alignment of the VTI12 family. Figure 2 Phylogenetic trees of ATG1 (a), ATG13 (b), VTI12 (c), and ATG18 (d). Different species belonging to the dicot and monocot lineages are marked with different symbols (empty symbol represents monocots and solid symbol represents dicots. M, monocotyledon; D, dicotyledon) (DOCX 6657 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Lingfei Shangguan
    • 1
  • Xiang Fang
    • 1
  • Lide Chen
    • 1
  • Liwen Cui
    • 1
  • Jinggui Fang
    • 1
  1. 1.Horticultural DepartmentNanjing Agricultural UniversityNanjingChina

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