Department of Biotechnology, Panjab University, Chandigarh, India.
Department of Biotechnology, Panjab University, Chandigarh, India; Department of Biology, University of Pennsylvania, Philadelphia, USA(1).
J Adv Res. 2022 Dec;42:17-28. doi: 10.1016/j.jare.2022.07.014. Epub 2022 Aug 3.
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.
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.
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.
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.
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.
复制事件是宿主-病原体相互作用中共同进化的基础。假基因（Ψs）是功能基因的无功能旁系同源物，而植物中的抗性基因（Rs）是解除致病入侵的关键。因此，破译植物防御中的假 R 基因的作用至关重要。
本研究旨在从功能上阐明葡萄全基因组复制衍生（WGD）的Ψs作为新型基因足迹以及作为葡萄基因组中重要基因调控因子的多种作用。
利用 PlantPseudo 管道和 HMM 分析鉴定与抗性基因（Ψ-Rs）相关的全基因组复制衍生的（WGD）Ψs。进一步利用与 Erysiphe necator 蛋白的蛋白质-蛋白质对接，对与真菌相关的新型抗真菌和抗菌肽进行了鉴定。预测了 Ψ-Rs 中的 miRNA 和 tasiRNA 靶位和转录因子（TF）结合位点。最后，使用 UPGMA 方法鉴定了 Ψ-Rs-lncRNA-编码基因的差异共表达模式。
从葡萄基因组的 31032 个 WGD Ψs 中鉴定出 2746 个 Ψ-Rs。从 Ψ-Rs 生成了 69 种抗菌肽和 81 种抗真菌肽。预测了五个新型抗真菌肽的潜在基因功能，并通过与 E. necator 蛋白对接进一步对其进行了鉴定。527 个抗性基因座特异性 Ψ-Rs 中的 395 个表现为亲本基因模拟物。此外，为了探索 Ψ-Rs 在植物防御中的多种作用，我们在这些 Ψ-Rs 上鉴定了 37026 个 TF 结合位点、208 个 miRNA 和 99 个 tasiRNA 靶位。194 个 Ψ-Rs 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，在病原体入侵过程中，79 个对病原体有反应的 Ψ-Rs 中有 6 个是重要的。
我们的研究提供了对病原体入侵至关重要的病原体反应性 Ψ-Rs，这将为未来的实验验证提供有用的资源。此外，我们从 Ψ-Rs 生成新型肽的发现为预测具有在植物系统中研究其生物活性的未来潜力的新型基因提供了有价值的见解。
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