Zia Komal, Sadaqat Muhammad, Ding Baopeng, Fatima Kinza, Albekairi Norah A, Alshammari Abdulrahman, Tahir Ul Qamar Muhammad
Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan.
College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China.
Front Genet. 2024 Feb 26;15:1358134. doi: 10.3389/fgene.2024.1358134. eCollection 2024.
Passion fruit is widely cultivated in tropical, subtropical regions of the world. The attack of bacterial and fungal diseases, and environmental factors heavily affect the yield and productivity of the passion fruit. The (CNL) gene family being a subclass of R-genes protects the plant against the attack of pathogens and plays a major role in effector-triggered immunity (ETI). However, no information is available regarding this gene family in passion fruit. To address the underlying problem a total of 25 and 21 genes have been identified in the genome of purple ( Sims.) and yellow () passion fruit respectively. Phylogenetic tree was divided into four groups with PeCNLs present in 3 groups only. Gene structure analysis revealed that number of exons ranged from 1 to 9 with 1 being most common. Most of the genes were clustered at the chromosome 3 and underwent strong purifying selection, expanded through segmental (17 gene pairs) and tandem duplications (17 gene pairs). genes contained elements involved in plant growth, hormones, and stress response. Transcriptome data indicated that and were found to be differentially expressed under Cucumber mosaic virus and cold stress. Three genes were validated to be multi-stress responsive by applying Random Forest model of machine learning. To comprehend the biological functions of PeCNL proteins, their 3D structure and gene ontology (GO) enrichment analysis were done. Our research analyzed the gene family in passion fruit to understand stress regulation and improve resilience. This study lays the groundwork for future investigations aimed at enhancing the genetic composition of passion fruit to ensure robust growth and productivity in challenging environments.
西番莲在世界热带、亚热带地区广泛种植。细菌和真菌病害的侵袭以及环境因素严重影响西番莲的产量和生产力。作为R基因子类的（CNL）基因家族可保护植物免受病原体侵袭，并在效应子触发免疫（ETI）中发挥主要作用。然而，关于西番莲中这个基因家族的信息尚无报道。为解决这一潜在问题，分别在紫色（西番莲）和黄色（西番莲）西番莲的基因组中鉴定出了25个和21个基因。系统发育树分为四组，PeCNLs仅存在于3组中。基因结构分析表明，外显子数量从1到9不等，其中1最为常见。大多数基因聚集在3号染色体上，经历了强烈的纯化选择，通过片段重复（17对基因）和串联重复（17对基因）进行扩增。基因包含参与植物生长、激素和应激反应的元件。转录组数据表明，在黄瓜花叶病毒和冷胁迫下，和被发现存在差异表达。通过应用机器学习的随机森林模型，验证了三个基因具有多胁迫响应性。为了解PeCNL蛋白的生物学功能，对其三维结构和基因本体（GO）富集分析进行了研究。我们分析了西番莲中的基因家族，以了解胁迫调控并提高抗逆性。本研究为未来旨在改善西番莲遗传组成以确保其在具有挑战性环境中稳健生长和生产力的研究奠定了基础。
