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Abstract Nucleotide-binding site (NBS) domain genes are one of the superfamily of resistance genes involved in plant responses to pathogens. The current study identified 12,820 NBS-domain-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes are classified into 168 classes with several novel domain architecture patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR, etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBSetc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG₀, OG₁, OG_2,etc.) and unique (highly specific to species; OG₈₀, OG_82,etc.) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG₂, OG_6,and OG₁₅in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to cotton leaf curl disease (CLCuD). The genetic variation between susceptible (Coker 312) and tolerant (Mac7)Gossypium hirsutumaccessions identified several unique variants inNBSgenes of Mac7 (6583 variants) and Coker312 (5173 variants). The protein–ligand and proteins-protein interaction showed a strong interaction of some putativeNBSproteins with ADP/ATP and different core proteins of the cotton leaf curl disease virus. The silencing ofGaNBS(OG₂) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful in understanding the plant adaptation mechanism. 

Abstract Cysteine-rich receptor-like-kinases (CRKs), a transmembrane subfamily of receptor-like kinase, play crucial roles in plant adaptation. As such cotton is the major source of fiber for the textile industry, but environmental stresses are limiting its growth and production. Here, we have performed a deep computational analysis ofCRKsin fiveGossypiumspecies, includingG. arboreum(60 genes), G. raimondii(74 genes), G. herbaceum(65 genes), G. hirsutum(118 genes), andG. barbadense(120 genes). All identified CRKs were classified into 11 major classes and 43 subclasses with the finding of several novel CRK-associated domains includingALMT, FUSC_2, Cript, FYVE,andPkinase. Of these,DUF26_DUF26_Pkinase_Tyrwas common and had elevated expression under different biotic and abiotic stresses. Moreover, the 35 land plants comparison identified several newCRKsdomain-architectures. Likewise, several SNPs and InDels were observed in CLCuD resistantG. hirsutum. The miRNA target side prediction and their expression profiling in different tissues predictedmiR172as a major CRK regulating miR. The expression profiling ofCRKsidentified multiple clusters with co-expression under certain stress conditions. The expression analysis under CLCuD highlighted the role ofGhCRK057, GhCRK059, GhCRK058, and GhCRK081in resistant accession. Overall, these results provided primary data for future potential functional analysis as well as a reference study for other agronomically important crops.