Browsing by Author "Aqsa Anwer Khan"

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    Genome-wide study of nucleotide-binding site resistance genes in land plants
    (UMT, Lhr, 2022) Aqsa Anwer Khan
    Plants are continuously revealed to a variety of biotic (bacteria, fungi, and oomycetes) and abiotic stresses. To survive, they developed a three-layered immune system. The physical layer, which is the first line of protection, is made up of the cell wall and the cuticles. The second line of defence is made up of pattern recognition receptors PRRs, and the third line of defence is made up of effector-induced immunity. The best type of defense is resistance (R) gene-dependent defense in which they recognize pathogen effectors and encounter it by activating a hypersensitive response. The majority of these R genes belong to the nucleotide-binding site (NBS) gene family which gives disease resistance to a variety of athogens. A genome-wide study was carried out in 34 land plants to identify putative NBS-containing genes and their evolutionary relationships among land plants. The analysis included identification, characterization, evolutionary study and expression profiling in different tissues under various stresses. A total of 12,823 genes were identified in thirtyfour land plants, a maximum number of NBS genes were observed in Medicago truncatula (XP) with 1206 genes and followed by Hordeum vulgare (891 genes), Populus trichocarpa (867 genes) and Oryza sativa with 794 genes and the lowest number of NBS was observed in Ginko bibola (11 genes). Interestingly, we did not found any NBS encoding genes in lower plants like Chlamydomonas reinhardtii and Amaranthus hypochondriacs L. Based on the conserved domains architecture in the primary sequence of proteins, we have classified all identified NBS genes into 21 major classes with 151 sub-classes. The major classes included class I (only NB-ARC domain; with 8128 genes), class II (NB-ARC with LRR motif; with 1606 genes), class III (TIR domain with NB-ARC; having 1506 genes), class IV (TIR--NB-ARC with LRR motif;with 486 genes), class V (RPW--NB-ARC domain; having 133 genes), class VI (Pkinase--NB- ARC domain; with 49 genes), class VII (NB-ARC--FNIP domain;having 27 genes), class VIII (NB-ARCā€”Pkinase domain; with 23 genes), class IX (NB-ARC--DDE_Tnp_4 domain; having 16 genes), class X (NBARC with Jacalin domain has 15 genes), class XI (NB-ARC with WRKY contain domain with 15 genes), class XII (Pkinase--NB-ARC with LRR motif having 15 genes), class XIII (TIR--NB-ARC with HSP70 domain with 15 genes), class XIV domain (NB-ARC with TIR domain contain 14 genes), class XV (NB-ARC with B3 domain having 10 genes), class XVI (NB-ARC with PAH domain has 8 genes), class XVII (Myb_DNA-binding with NB-ARC domain with 6 genes), class XVIII (NB-ARC with PP domain contain 6 genes), class XIX (NB-ARC with Thioredoxin domain has 6 genes), class XX (zf-BED with NBARC domain contain 6 genes). The most commonly found classes are NBS, NL, TNL and TN. For the evolutionary study, we included only 33 plants. The evolutionary analysis included orthogroups, orthologs, gene duplication events, orthogroup duplications, orthologs overlapping, xenologs, paralogs etc. The expression profiling of nucleotidebinding site genes in Gossypium hirsutum, Gossypium arboreum, Arabidopsis thaliana and Zea mays, under different biotic (CLCuD) and abiotic stresses, as well as developmental stages, was performed in different (tissues, root, leaf, stem, and ovule) at different time intervals (10 DPA, 15DPA, 20DPA), showed their putative role in growth, development and plant adaptation. The SNP/InDels gene variation between tolerant and susceptible cultivars also demonstrated a clear divergence showing many unique SNPs/InDels. The molecular docking of ATPs and ADPs with putative NBS genes in cotton were also assessed through Ligand-receptor interaction analysis