AUTHOR=Tahir ul Qamar Muhammad , Sadaqat Muhammad , Zhu Xi-Tong , Li Huan , Huang Xing , Fatima Kinza , Almutairi Mashal M. , Chen Ling-Ling 

TITLE=Comparative genomics profiling revealed multi-stress responsive roles of the CC-NBS-LRR genes in three mango cultivars

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1285547

DOI=10.3389/fpls.2023.1285547

ISSN=1664-462X

ABSTRACT=<p>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 <italic>Mangifera indica</italic> cultivars (<italic>Alphonso, Hong Xiang Ya</italic>, and <italic>Tommy atkins</italic>) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from <italic>H. Xiang Ya</italic>, and 1266 genes and 2098 PAVs from <italic>T. atkins</italic> 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 <italic>Alphonso</italic>, <italic>H. Xiang Ya</italic>, and <italic>T. atkins</italic> respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All <italic>MiCNL</italic> 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 <italic>cis</italic>-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 <italic>Mi_A_CNL13</italic> and <italic>14</italic> were up-regulated while <italic>Mi_A_CNL15, 25, 30, 31</italic>, and <italic>40</italic> were down-regulated in disease stress. On the other hand, <italic>Mi_A_CNL2, 14, 41</italic>, and <italic>45</italic> were up-regulated and <italic>Mi_A_CNL47</italic> is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of <italic>MiCNLs</italic>. It was found that <italic>Mi_A_CNL14</italic> 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.</p>