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

中文翻译：

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全基因组鉴定的III类POD基因家族及其在葡萄树中的表达谱（Vitis vinifera L）。

III类过氧化物酶（POD）参与广泛的生理活动，例如木质素的形成，细胞壁成分，对致病性或草食动物的防御以及非生物胁迫耐受性。对POD家族成员进行了充分的研究，并通过几种植物物种的生物信息学分析对其进行了表征，但是迄今为止，尚未对该葡萄中的该基因家族进行过全基因组范围的分析。我们在葡萄基因组中全面鉴定了47种POD，并根据它们的系统发育分析将其进一步分为7个亚组。基序组成和基因结构组织分析结果表明，同一亚组中的POD具有相似的结合，而蛋白质序列高度保守。有趣的是 染色体作图和基因共线性分析的综合分析表明，分散和串联重复事件都有助于葡萄中PODs的扩增。同样，基因重复分析表明，大多数基因（20）是分散的，随后依次是（15）串联，（9）分段或全基因组重复和（3）近端。POD的进化分析，例如15个重复基因对的Ka / Ks比小于1.00，表明大多数表现出纯化选择的基因对和7对正选择值大于1.00的基因。基因本体富集（GO），京都基因全基因组百科全书（KEGG）分析和顺式元素预测也揭示了POD在植物生长和发育活动中的积极作用，以及对压力刺激的反应。此外，基于可公开获得的RNA序列数据，PODs在几个发育阶段的组织特异性应答中的表达模式显示出不同的表达模式。随后，针对30种基因（NaCl，干旱和ABA）选择了用于RT-PCR验证的基因，这些基因显示了它们在葡萄中的关键作用。总之，我们预测这些结果将导致有关葡萄遗传改良的新见解。