Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsIn conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.
Highlights
MethodsIdentification of POD genes family in grapevine In order to identify the POD genes, we used the 73 reference sequences of Arabidopsis against grapevine (genome version 2.1) with the help of BioEdit tools
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
Characterization of POD gene family in grapevine In this study, a total of 47 POD genes were identified from the grapevine genome and for simplicity, we denominated as VvPOD1-VvPOD47 based on their orthologous position with Arabidopsis thaliana
Summary
Identification of POD genes family in grapevine In order to identify the POD genes, we used the 73 reference sequences of Arabidopsis against grapevine (genome version 2.1) with the help of BioEdit tools. Www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and SMART databases (http://smart.embl-heidelberg.de/) [44]. Those sequences with absent of POD domains and sequence with obvious error in length (>100aa length) were eliminated from the study before analysis. Phylogenetic analysis of POD gene family For phylogenetic characterization, the multiple sequences alignment (MSA) of PODs was performed by MUSCLE [45] using MEGA 7.0 software with the default options [46]. After scrutiny of several models in MEGA 7.0, we choose the Jones, Taylor, and Thornton amino acid substitution model (JTT model) and for the reliability of resulting phylogenetic tree, the bootstrap values of 1000 replications were performed and keeping the other parameters as a default
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