Tahir Ul Qamar Muhammad, Sadaqat Muhammad, Zhu Xi-Tong, Li Huan, Huang Xing, Fatima Kinza, Almutairi Mashal M, Chen Ling-Ling
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.
Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan.
Front Plant Sci. 2023 Oct 30;14:1285547. doi: 10.3389/fpls.2023.1285547. eCollection 2023.
The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three cultivars (, and ) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from , and 1266 genes and 2098 PAVs from were added to the reference genome. For the identification of CC-NBS-LRR (CNL) genes in these mango cultivars, this draft pan-genome study has successfully identified 47, 27, and 36 members in , , and respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All genes are unevenly distributed on chromosomes. Both tandem and segmental duplication events played a significant role in the expansion of the CNL gene family. These genes contain -elements related to light, stress, hormone, and development. The analysis of protein-protein interactions (PPI) revealed that MiCNL proteins interacted with other defense-responsive proteins. Gene Ontology (GO) analysis indicated that MiCNL genes play a role in defense mechanisms within the organism. The expression level of the identified genes in fruit peel was observed under disease and cold stress which showed that and were up-regulated while , and were down-regulated in disease stress. On the other hand, , and were up-regulated and is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of . It was found that is a gene that responds to multiple stress conditions. The CNLs have similar protein structures which show that they are involved in the same function. The above findings provide a foundation for a deeper understanding of the functional characteristics of the mango CNL gene family.
核苷酸结合位点富含亮氨酸重复序列（NBS-LRR）基因家族是植物中最大的抗病（R）基因群体，在响应通常参与效应子触发免疫（ETI）的病毒、细菌和真菌时具有活性。泛基因组范围的研究使研究人员能够同时分析多个物种或其成员的遗传多样性，从而全面了解它们之间的进化关系和多样性。构建了三个品种（、和）的泛基因组草图，并通过ppsPCP流程筛选了存在/缺失变异（PAV）。结果，来自的2823个基因和5907个PAV以及来自的1266个基因和2098个PAV被添加到参考基因组中。为了鉴定这些芒果品种中的CC-NBS-LRR（CNL）基因，这项泛基因组草图研究分别成功鉴定出、和中的47个、27个和36个成员。系统发育分析将MiCNL蛋白分为四个不同的亚组。所有基因在染色体上分布不均。串联重复和片段重复事件在CNL基因家族的扩展中都发挥了重要作用。这些基因含有与光、胁迫、激素和发育相关的元件。蛋白质-蛋白质相互作用（PPI）分析表明，MiCNL蛋白与其他防御反应蛋白相互作用。基因本体（GO）分析表明，MiCNL基因在生物体的防御机制中发挥作用。在病害和冷胁迫下观察了所鉴定基因在果皮中的表达水平，结果表明，在病害胁迫下，和上调，而、和下调。另一方面，在冷胁迫下，、和上调，而下调。随后，使用随机森林（RF）分类器评估的多胁迫响应。发现是一个对多种胁迫条件有响应的基因。CNL具有相似的蛋白质结构，表明它们参与相同的功能。上述发现为深入了解芒果CNL基因家族的功能特性奠定了基础。
