Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions,Journal of Advanced Research

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Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions
Journal of Advanced Research ( IF 11.4 ) Pub Date : 2022-08-03 , DOI: 10.1016/j.jare.2022.07.014
Naina Garewal ₁ , Shivalika Pathania ₁ , Garima Bhatia ₂ , Kashmir Singh ₁

Affiliation

Introduction

Duplication events are fundamental to co-evolution in host-pathogen interactions. Pseudogenes (Ψs) are dysfunctional paralogs of functional genes and resistance genes (Rs) in plants are the key to disarming pathogenic invasions. Thus, deciphering the roles of pseudo-R genes in plant defense is momentous.

Objectives

This study aimed to functionally characterize diverse roles of the resistance Ψs as novel gene footprints and as significant gene regulators in the grapevine genome.

Methods

PlantPseudo pipeline and HMM-profiling identified whole-genome duplication-derived (WGD) Ψs associated with resistance genes (Ψ-Rs). Further, novel antifungal and antimicrobial peptides were characterized for fungal associations using protein–protein docking with Erysiphe necator proteins. miRNA and tasiRNA target sites and transcription factor (TF) binding sites were predicted in Ψ-Rs. Finally, differential co-expression patterns in Ψ-Rs-lncRNAs-coding genes were identified using the UPGMA method.

Results

2,746 Ψ-Rs were identified from 31,032 WGD Ψs in the genome of grapevine. 69-antimicrobial and 81-antifungal novel peptides were generated from Ψ-Rs. The putative genic potential was predicted for five novel antifungal peptides which were further characterized by docking against E. necator proteins. 395 out of 527 resistance loci-specific Ψ-Rs were acting as parental gene mimics. Further, to explore the diverse roles of Ψ-Rs in plant-defense, we identified 37,026 TF-binding sites, 208 miRNA, and 99 tasiRNA targeting sites on these Ψ-Rs. 194 Ψ-Rs were exhibiting tissue-specific expression patterns. The co-expression network analysis between Ψs-lncRNA-genes revealed six out of 79 pathogen-responsive Ψ-Rs as significant during pathogen invasion.

Conclusions

Our study provides pathogen responsive Ψ-Rs integral for pathogen invasion, which will offer a useful resource for future experimental validations. In addition, our findings on novel peptide generations from Ψ-Rs offer valuable insights which can serve as a useful resource for predicting novel genes with the futuristic potential of being investigated for their bioactivities in the plant system.

中文翻译：

葡萄中 Pseudo-R 基因的鉴定及其在宿主-病原体相互作用中作为免疫调节剂的作用的表征

介绍

复制事件是宿主-病原体相互作用共同进化的基础。假基因 ( Ψs ) 是植物中功能基因和抗性基因 ( Rs ) 的功能失调的旁系同源物，是消除病原体入侵的关键。因此，破译伪 R基因在植物防御中的作用具有重要意义。

目标

本研究旨在从功能上表征抗性ψ作为新基因足迹和作为葡萄基因组中重要基因调节因子的不同作用。

方法

PlantPseudo 管道和 HMM 分析确定了与抗性基因 ( ψ-Rs ) 相关的全基因组复制衍生 (WGD) ψs。此外，新型抗真菌和抗菌肽的特征在于使用蛋白质与白粉病菌蛋白的蛋白质对接与真菌相关。在Ψ-Rs中预测了 miRNA 和 tasiRNA 靶位点和转录因子 (TF) 结合位点。最后，使用 UPGMA 方法鉴定了Ψ-Rs -lncRNAs 编码基因中的差异共表达模式。

结果

从葡萄基因组中的31,032 个 WGD Ψs中鉴定出2,746个 Ψ-Rs 。从Ψ-Rs中产生了 69 种抗微生物和 81 种抗真菌新肽。预测了五种新型抗真菌肽的推定基因潜力，这些肽通过与E. necator蛋白对接进一步表征。527 个抗性位点特异性Ψ-R中有 395 个充当亲代基因模拟物。此外，为了探索Ψ-Rs在植物防御中的不同作用，我们在这些 Ψ-Rs 上确定了 37,026 个 TF 结合位点、208 个 miRNA 和 99 个 tasiRNA 靶向位点。第194章表现出组织特异性表达模式。Ψs -lncRNA 基因之间的共表达网络分析显示，在病原体入侵期间，79 个病原体反应性Ψ-Rs中有 6 个具有重要意义。