Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

Abstract

Background: The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

Results: We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

Conclusions: In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

Keywords: Collinearity and expression analysis; Genome-wide analysis; Grapevine; POD genes family.

Fig. 1

Phylogenetic relationship of POD genes between grapevine and Arabidopsis. The phylogenetic tree was constructed by MEGA 7.0 using the Maximum Likelihood Method (1000 bootstrap)

Fig. 2

a and b. a Motif composition of POD in grapevine are presented in different color ranging from motif 1–10. b The coding sequences (CDS) and untranslated regions (UTR) for PODs in grapevine are represented by yellow and green boxes, respectively. Motif composition and gene structure were visualized by TBtools software. At the bottom of the figure, the relative position is proportionally displayed based on the kilobase scale

Fig. 3

a and b. a The chromosomal localizations are shown for grapevine (Chr01–19) is blue and for Arabidopsis different random colors. b The collinear correlation at the center for all the POD genes is displayed between grapevines and Arabidopsis. The green line indicates the collinear relationship among VvPODs and AtPODs, blue represent the relation within VvPOD and red lines indicates the tandem duplications

Fig. 4

Expression profiles of the 47 POD genes in grapevine, including different organs, tissues, and developmental stages. Data were normalized based on the mean expression value of each gene in all tissues analyzed. BerryPericarp-FS: berry pericarp fruit set; BerryPericarp-PFS: berry pericarp post-fruit set; BerryPericarp-V: Bud-S: bud swell; Bud-B: bud burst (green tip); Bud-AB: bud after-burst (rosette of leaf tips visible); Bud-L: latent bud; Bud-W: winter bud; Flower-FB: flowering begins (10% caps off); Flower-F: flowering (50% caps off); Leaf-Y: young leaf (pool of leaves from shoot of 5 leaves); Leaf-FS: mature leaf (pool of leaves from shoot at fruit set); Rachis-FS: rachis fruit set; Rachis-PFS: rachis post fruit set; Stem-G: green stem; Stem-W: woody stem; Tendril-Y: young tendril (pool of tendrils from shoot of 7 leaves); Tendril-WD: well developed tendril (pool of tendrils from shoot of 12 leaves); Tendril-FS: mature tendril (pool of tendrils at fruit set)

Fig. 5

a Relative expression profiling by RT-PCR for significantly up and down-regulated genes under various abiotic stress (i.e., NaCl, PEG, and ABA). b Pearson’s correlation coefficients (PCCs) of 30 VvPOD genes against abiotic stress such as NaCl, PEG, and ABA and were illustrated by using RStudio