Genome-Wide Identification and Characterisation of Stress-Associated Protein Gene Family to Biotic and Abiotic Stresses of Grapevine

Abstract

Grapevine is one of the earliest domesticated fruit crops and prized for its table fruits and wine worldwide. However, the concurrence of a number of biotic/abiotic stresses affects their yield. Stress-associated proteins (SAPs) play important roles in response to both biotic and abiotic stresses in plants. Despite the growing number of studies on the genomic organisation of SAP gene family in various species, little is known about this family in grapevines (Vitis vinifera L.). In this study, a total of 15 genes encoding proteins possessing A20/AN1 zinc-finger were identified based on the analysis of several genomic and proteomic grapevine databases. According to their structural and phylogenetics features, the identified SAPs were classified into three main groups. Results from sequence alignments, phylogenetics, genomics structure and conserved domains indicated that grapevine SAPs are highly and structurally conserved. In order to shed light on their regulatory roles in growth and development, as well as the responses to biotic/abiotic stresses in grapevine, the expression profiles of SAPs were examined in publicly available microarray data. Bioinformatics analysis revealed distinct temporal and spatial expression patterns of SAPs in various tissues, organs and developmental stages, as well as in response to biotic/abiotic stresses. This study provides insight into the evolution of SAP genes in grapevine and may aid in efforts for further functional identification of A20/AN1-type proteins in the signalling cross-talking induced by biotic/abiotic stresses.

Keywords: SAP gene family; abiotic stress; biotic stress; genome-wide; grapevine; transcript analysis.

Figure 1

Conserved motif arrangement in grapevine SAP proteins according to the phylogenetic relationship. (A) Conserved motif distributions of the VvSAP proteins annotated with the MEME server. Ten motifs are marked by different colours; (B) analysis of conserved domains of VvSAP proteins; (C) analysis of cis-regulatory elements of VvSAP protein; (D) analysis of VvSAP protein coding.

Figure 2

Distribution of the VvSAP genes among eight grapevine chromosomes. The scale on the left represents the length of each chromosome displayed in megabase (Mb). Tandemly duplicated genes are coloured with red.

Figure 3

Phylogenetic analysis of SAP proteins from grapevine (V. vinifera) and other two plants (A. thaliana and O. sativa). Sequence alignment was performed with full-length SAP amino acid sequences from different plant species using MAFFT as the default parameters, and the neighbour-joining (NJ) phylogenetic tree was created by MEGA 7.0 using a bootstrap option of 1000 replications.

Figure 4

Alignment of conserved domains of SAP family in V. vinifera. Alignment of conserved A20/AN1 and grapevine SAP protein sequences. Identical proteins are highlighted in red boxes.

Figure 5

Expression levels of VvSAP genes in different tissues of grapevine. Abbreviations stand for plant developmental stages, where FS stands for fruit set, PFS for post-fruit set, V for veraison, MR for mid-ripening, R for ripening, PHWI for post-harvest withering I (1st month), BerryPericarp-PHWII for post-harvest withering II (2nd month) and BerryPericarp-PHWIII for post-harvest withering III (3rd month), Y stands for Young, FB stands for flowering begins, F stands for flowering, ML stands for mature leaf, WD stands for well developed, W stands for woody, S represents different developmental stages in Bud and Leaf, swell in bud and senescence in leaf. Black lines indicate reproductive and vegetative organs, respectively. The colour scale represents log 2 expression values.

Figure 6

Expression of VvSAPs under biotic stresses. VvSAPs of V. rupestris expressing GFP-AtTUB6 under the infection of culture filtration of N. parvum Bt-67 and B. dothidea Sd-18 at 12 hpi (A); N. parvum Bt-67 and D. seriata 98.1 at 3 dpi (B); and VvSAPs of V. aestivalis × V. vinifera ‘Norton’ and V. vinifera ‘Cabernet Sauvignon’ under infection of conidiospores of Erysiphe necator (C). cf, culture filtration, cs conidiospores, con, control. The expression level of genes was determined based on the value of FPKM. The colour scale represents log 2 expression values.

Figure 7

Expression of VvSAPs under abiotic stresses. Expression analysis of VvSAPs under drought, salt (match water potential to those of the water-deficit-treated plants), and cold (5 ℃) stresses in grapevine in short-term treatment (A); and long-term treatment (B). The expression level of genes was determined based on the value of RPKM. The colour scale represents log 2 expression values.