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.

Recent Developments in Enzymatic Antioxidant Defence Mechanism in Plants with Special Reference to Abiotic Stress

“…To understand the correlation between the stress memory and activity of POX (among other antioxidant enzymes), Alopecurus pratensis was given intermittent drought treatment, and it was found that drought memory is linked to higher levels of antioxidative enzymes, including POX, SOD and CAT [ 85 ]. Recently, a paper posted on a pre-print server (not peer reviewed) revealed 47 POX genes in the grapevine genome, classified into seven subgroups based on their phylogenetic analysis and GWAS approach [ 86 ]. After studying horseradish POX under in vitro conditions, three different reaction mechanisms catalysed by POX were proposed by Jovanović et al [ 87 ], i.e., Peroxidatic, oxidative and hydroxylic cycles, which are described in Figure 3 .…”

Low‐dose prestorage 24‐epibrassinolide spray enhances postharvest chilling tolerance in zucchini squash ( Cucurbita pepo L.) by eliciting peroxidase and phenolic antioxidants

“…In line with that, the current study, EBR-treated fruit showed an increased peroxidase (POD) activity during the shelflife period following the chilling stress (Figure 7). POD is a ubiquitous enzyme having multiple roles in plants (Xiao et al, 2020).…”

Peer Review #1 of "Transcriptome analysis revealed gene regulatory network involved in PEG-induced drought stress in Tartary buckwheat (Fagopyrum Tararicum) (v0.1)"

“…Previous studies have supported that LEA proteins were involved in protecting higher plants from damage caused by environmental stresses, especially drought, by acting as antioxidants and membrane and protein stabilizers during water stress (Hong-Bo et al, 2005;Tunnacliffe & Wise 2007). Genes encoding H 2 O 2 scavengers, such as CAT, SOD and POD were also involved in the adaptation of plant drought responses (Luna et al, 2005;Molina-Rueda et al, 2013;Xiao et al, 2020). Many TFs, including ABRE2, RD29B, RD20A, MYB2, MBC2, RD26, DREB1D, HB, RD22, DREB2, NAC, and bZIP TFs (Fu et al, 2016;Lee et al, 2010;Roychoudhury et al, 2013;Shinozaki & Yamaguchi-Shinozaki 2007;Yamaguchi-Shinozaki & Shinozaki 2005) regulated plant drought resistance through two regulatory pathways: the ABA-dependent pathway and ABA-independent pathway (Abdel-Ghany et al, 2020;Du et al, 2010;Frey et al, 2012;Li et al, 2008;Roychoudhury et al, 2013;Shi et al, 2020;Shinozaki & Yamaguchi-Shinozaki 2007).…”