PDF(Pubmed)
Abstract：
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 Mangifera indica cultivars (Alphonso, Hong Xiang Ya, and Tommy atkins) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from H. Xiang Ya, and 1266 genes and 2098 PAVs from T. atkins 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 Alphonso, H. Xiang Ya, and T. atkins respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All MiCNL 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 cis-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 Mi_A_CNL13 and 14 were up-regulated while Mi_A_CNL15, 25, 30, 31, and 40 were down-regulated in disease stress. On the other hand, Mi_A_CNL2, 14, 41, and 45 were up-regulated and Mi_A_CNL47 is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of MiCNLs. It was found that Mi_A_CNL14 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.
摘要：
核苷酸结合位点-富含亮氨酸的重复序列（NBS-LRR）基因家族是植物中最大的一组抗病性（R）基因，并且对病毒具有反应活性，细菌,和真菌通常参与效应子触发免疫（ETI）。全基因组研究允许研究人员同时分析多个物种或其成员的遗传多样性，全面了解它们之间的进化关系和多样性。三个印度芒果品种的泛基因组草案（Alphonso，洪香雅,和Tommyatkins）构建，并通过ppsPCP管道过滤存在/不存在变体（PAV）。因此,来自H.香雅的2823个基因和5907个PAV，来自T.atkins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，这项泛基因组研究草案已经成功确定了阿方索的47、27和36名成员，H.向雅，分别是T.atkins.系统发育分析将MiCNL蛋白分为四个不同的亚组。所有MiCNL基因在染色体上分布不均匀。串联和分段复制事件在CNL基因家族的扩展中起着重要作用。这些基因含有与光相关的顺式元件，压力，激素，和发展。蛋白质-蛋白质相互作用（PPI）的分析表明，MiCNL蛋白与其他防御响应蛋白相互作用。基因本体论（GO）分析表明MiCNL基因在生物体内的防御机制中起作用。在疾病和冷胁迫下观察到果皮中鉴定基因的表达水平，表明Mi_A_CNL13和14上调，而Mi_A_CNL15、25、30、31和40下调。疾病应激。另一方面,在冷胁迫下，Mi_A_CNL2、14、41和45上调，Mi_A_CNL47下调。随后，随机森林(RF)分类器用于评估MiCNL的多应激反应。发现Mi_A_CNL14是响应多种胁迫条件的基因。CNL具有相似的蛋白质结构，表明它们参与相同的功能。上述发现为更深入地理解芒果CNL基因家族的功能特征奠定了基础。
