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

- Genome-wide identification of the class III POD gene family and their expression.
- profiling in grapevine ( Vitis vinifera L).
- 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..
- 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.
- Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine..
- Keywords: Grapevine, Genome-wide analysis, POD genes family, Collinearity and expression analysis.
- Full list of author information is available at the end of the article.
- Peroxidases (EC 1.11.1.X) is a group of well-known large multi-gene family and that are broadly dispersed in liv- ing organisms.
- The class III plant peroxidase (POD) plant is a plant-specific oxidoreductas, which is one of the many types of peroxidases that are widely distributed in animals, plants and microorganisms [3.
- However, the direct role of this multi-gene family is still elusive and only a few studies have demonstrated their functional role .
- The overexpression of the POD genes in A.
- Nevertheless, to date, no previous genome-wide analysis has been car- ried out of this gene family in grapevine.
- A common goal of current plant genomics research is to create an expand- able platform for global classification and analysis of plant gene family.
- In the meantime, the availability of the grapevine genome (Version 2.1) facili- tate the research in grapevine momentously for its gen- etic studies by improvement in the quality of berry..
- In the present study, we performed a wide-ranging bioinformatics analysis of POD gene family and verified their role against various stress responses (i-e., NaCl, drought, and ABA) in grapevine.
- In general, the results of our study will undoubtedly be helpful for future re- search on fruits crop species and pay the base for func- tional characterization of the PODs gene family..
- Characterization of POD gene family in grapevine.
- While, the gene duplication types (i.e., dispersed, tandem, proximal, and segmental or whole-genome duplication) and subcellular localization analysis were also briefly studied for each of POD proteins (Supplementary Table S1).
- variability was observed in most of the genes for GRAVY, indicating mostly hydrophilic properties and only a few of them (VvPOD46, VvPOD43, VvPOD31, and VvPOD25) are hydrophobic in nature by showing positive values.
- Additionally, the gene duplication analysis intimated that most of the genes (20) were dispersed followed by tandem (15), segmental or whole-genome duplication (9), and proximal (3), respectively..
- Phylogenetic relationships, gene structure organization of POD gene family in grapevine.
- 1 Phylogenetic relationship of POD genes between grapevine and Arabidopsis.
- For instance, we observed that subgroup 7 contains the most number of genes (15 and 17) as compared to other subgroups in grapevine and Arabidopsis.
- Further, these findings indicated the structural diversification among VvPOD gene family..
- Chromosomal localization, gene collinearity, and Ka/Ks analysis of POD.
- 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.
- At the bottom of the figure, the relative position is proportionally displayed based on the kilobase scale.
- Results showed that most of the gene pairs having less than 1.00 Ka/Ks ratio suggested purifying selection, thus revealed lim- ited divergence after gene duplications.
- Gene ontology enrichment (GO), Kyoto encyclopedia of genes genomics (KEGG) and cis-regulatory elements analysis in grapevine.
- Similarly, for CC processes and BP most of the GO terms are re- sponsive to “cell wall, plasmodesma, symplast, cell-cell junction, plant-type cell wall” (GO:0005618, GO:.
- Additionally, the KEGG enrichment analysis indicated the three major pathways among PODs in grapevine such as “Biosynthesis of other secondary metabolites, phenylpropanoid biosynthesis, and metabolism” (Supple- mentary Table S3)..
- Moreover, the cis-acting elements in the promoter region of POD members were performed by using the PlantCARE database.
- In brief, most of the genes were largely participating in light regulation with key regu- latory elements (GT1-motif, G-Box, GATA-motif, and AE-Box), followed by hormones (CGTCA-motif, TGACG-motif, ABRE, and GARE-motif), stress and other regulatory factors (LTR, ARE, CCAAT-Box, CAT-BOX, o2-site.
- Thus, we observed the diversified role of POD members and their indirect involvement in several biotic- abiotic/hormone signaling processes (Supplementary Table S4)..
- 1 The POD genes in grapevine with outlier Ka/Ks and various types of duplications of the POD gene pairs with the detection by the MCScan algorithm (i.e., Dispersed, proximal, tandem, and segmental).
- Expression profiling of POD genes in different organs and developmental stages in grapevine.
- The expression profiling of all 47 PODs in grapevine de- rived from 19 tissues and organs during their develop- mental stages were investigated in the present srudy..
- Moreover, the rest of the genes showed either moderate or weak expression abundance in all the selected tissues and organs, speculating their limited response in grapevine..
- qRT-PCR analysis of POD genes in response to (NaCl, drought, and ABA).
- In response to salt stress, approximately 52% of the total genes showed higher ex- pression level, whereas the rest of the genes showed ei- ther moderate or low expression.
- Most of the genes decreased their expression at the early stress periods (1 h and 12 h), but they tended to increase their expression afterwards (24 h).
- Moreover, the correlation analysis based on Pearson ’ s Correlation Coefficient (PCC) of the relative expression indicated largely a highly positive correlation and some of them were found with inverse correlation (Fig.
- Taken together, these results of POD genes based on ex- pression level respond to multiple stresses and might play an important role in the maintenance of plant growth..
- The PODs multi-gene family are involved in the various biological process by regulating plant growth and devel- opmental processes.
- However, to date, no previous bioinformatics analysis have been carried out in grapevine for this important gene family.
- Also, the available genomic resources for grapevine (http://ge- nomes.cribi.unipd.it/grape/) provides useful information and tools for the analysis of POD gene family in grape- vine.
- In this study, a total of 47 POD genes were identi- fied in grapevine and is known to be the largest gene families in woody plants [25].
- We comprehensively ana- lyzed physicochemical properties, phylogenetic relation- ships, chromosomal mapping, gene collinearity analysis, motif composition and gene structure organization, and evolutionary analysis for the duplicated pairs of POD..
- GO, KEGG, cis-regulatory elements, expression profiling of spatio-temporal response, and qRT-PCR analysis in response to (NaCl, drought, and ABA) disclosed exten- sive information on the gene functions and expression dynamics of tissue-specific and abiotic stress response in grapevine..
- Moreover, the comparative structure analysis of POD showed that same subgroup shared a common junction..
- These results indicated a possible structural diversifica- tion within VvPOD gene family, which plays an import- ant role during the evolution of multi-gene family [30]..
- Similarly, in the process of evolutionary history, most of the higher plant underwent polyploidization that is vital ingredient in shaping plant genome [34].
- In this study, the types of duplications in grapevine were identified by the help of MCScanX among POD genes.
- segmental and tandem duplication plays a critical role in the expansion of gene family .
- POD gene family in grapevine.
- 4 Expression profiles of the 47 POD genes in grapevine, including different organs, tissues, and developmental stages.
- Results inferred that 15 pairs of POD have shown less than 1.00 Ka/Ks ratio, indicating purifying selection and 7 pairs exhibiting more than 1.00 suggested the posi- tive selection.
- The rest of the other genes showed down- regulation with similar tendency throughout grapevine tis- sues and organs developmental phases..
- Salt stress is one of the severe.
- This suggested their important roles in grapevine against abiotic stresses.
- In conclusion, we systematically identified a total of 47 POD genes in grapevine and were categorized into 7 subgroups, as supported by phylogenetic analysis.
- The GO, KEGG, and cis-elements analysis also extended our repositories on the diverse functions of PODs in plant developments during various stress-related activities in grapevine.
- While, the transcriptional profiling of various organs during several developmental stages and RT-PCR analysis, provide a stand-point of the PODs in improving the plant growth.
- Thus, the results of our study increase our understanding of POD genes in grapevine and laying the solid foundation for genetic improvement in other fruit crops..
- Identification of POD genes family in grapevine.
- Those sequences with absent of POD domains and se- quence with obvious error in length (>100aa length) were eliminated from the study before analysis..
- Phylogenetic analysis of POD gene family.
- The various types of duplications of the POD gene pairs were detected by the MCScan algorithm..
- Gene structure, motifs composition, and physicochemical analysis of POD protein.
- For the gene structure illustration, we utilized the GFF3 file of the grapevine genome and images were imple- mented by TBtools software [47].
- The motifs analysis of POD protein were performed by the Multiple Em of Motif Elicitation (MEME Suite) version 5.0.5 and then demonstrated by TBtools software.
- Gene ontology (GO), Kyoto encyclopedia of genes and genomics (KEGG) and cis-elements predictions of class III peroxidase gene family.
- Available on- line: http://genomes.cribi.unipd.it/grape/, V2.1), was uti- lized for the chromosomal locations of POD genes and were mapped based on information available.
- RNA isolation and transcriptional profiling of POD gene family in grapevine.
- The basic information of POD genes identified in grapevine.
- The gene ontology of POD gene in grapevine.
- Kyoto Encyclopedia of Genes and Genomics (KEGG) POD genes in grapevine.
- Cis-Elements of POD genes in grape- vine.
- The FPKM based values of POD genes in grapevine in- cluding, different organs, tissues, and developmental stages.
- Relative expression patterns (log 2 ) of POD genes in grapevine by qRT- PCR.
- Sequences of the POD gene primers used for quantitative real-time PCR..
- Evolution and expression of class III peroxidases.
- Cloning and molecular characterization of the basic peroxidase isoenzyme from Zinnia elegans, an enzyme involved in lignin biosynthesis.
- Bioinformatic and functional characterization of the basic peroxidase 72 from Arabidopsis thaliana involved in lignin biosynthesis.
- Genes encoding plant-specific class III peroxidases are responsible for increased cold tolerance of the brassinosteroid- insensitive 1 mutant.
- Analysis and expression of the class III peroxidase large gene family in Arabidopsis thaliana.
- Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response.
- Structural, evolutionary, and functional analysis of the class iii peroxidase gene family in chinese pear (Pyrus bretschneideri).
- Genome- wide identification and expression profiling of the polygalacturonase (PG) and pectin methylesterase (PME) genes in grapevine (Vitis vinifera L.
- Characterization of class iii peroxidases from switchgrass.
- The class III peroxidase (pod) gene family in cassava: identification, phylogeny, duplication, and expression.
- Genome-wide identification, characterization and expression analysis of the chalcone synthase family in maize.
- Genome-wide identification, evolution, and transcriptional profiling of PP2C gene family in Brassica rapa.
- Genome-wide identification, phylogeny and expression profiling of class III peroxidases gene family in Brachypodium distachyon.
- Evolution and expression divergence of E2 gene family under multiple abiotic and phytohormones stresses in Brassica rapa.
- Genome-wide identification, classification, and expression pattern of homeobox gene family in Brassica rapa under various stresses.
- Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress

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