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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. 

Summary IRE1, BI‐1, and bZIP60 monitor compatible plant–potexvirus interactions though recognition of the viral TGB3 protein. This study was undertaken to elucidate the roles of threeIRE1isoforms, thebZIP60UandbZIP60S, andBI‐1roles in genetic reprogramming of cells during potexvirus infection.Experiments were performed usingArabidopsis thalianaknockout lines andPlantago asiatica mosaic virusinfectious clone tagged with the green fluorescent protein gene (PlAMV‐GFP).There were more PlAMV‐GFP infection foci inire1a/b,ire1c,bzip60, andbi‐1knockout than wild‐type (WT) plants. Cell‐to‐cell movement and systemic RNA levels were greaterbzip60andbi‐1than in WT plants. Overall, these data indicate an increased susceptibility to virus infection. Transgenic overexpression ofAtIRE1borStbZIP60inire1a/borbzip60mutant background reduced virus infection foci, whileStbZIP60expression influences virus movement. Transgenic overexpression ofStbZIP60also confers endoplasmic reticulum (ER) stress resistance following tunicamycin treatment. We also show bZIP60U and TGB3 interact at the ER.This is the first demonstration of a potatobZIPtranscription factor complementing genetic defects in Arabidopsis. Evidence indicates that the three IRE1 isoforms regulate the initial stages of virus replication and gene expression, while bZIP60 and BI‐1 contribute separately to virus cell‐to‐cell and systemic movement. 

Abstract Zinc finger (Zf)-BED proteins are a novel superfamily of transcription factors that controls numerous activities in plants including growth, development, and cellular responses to biotic and abiotic stresses. Despite their important roles in gene regulation, little is known about the specific functions of Zf-BEDs in land plants. The current study identified a total of 750 Zf-BED-encoding genes in 35 land plant species including mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. The gene family size was somewhat proportional to genome size. All identified genes were categorized into 22 classes based on their specific domain architectures. Of these, class I (Zf-BED_DUF-domain_Dimer_Tnp_hAT) was the most common in the majority of the land plants. However, some classes were family-specific, while the others were species-specific, demonstrating diversity at different classification levels. In addition, several novel functional domains were also predicated including WRKY and nucleotide-binding site (NBS). Comparative genomics, transcriptomics, and proteomics provided insights into the evolutionary history, duplication, divergence, gene gain and loss, species relationship, expression profiling, and structural diversity of Zf-BEDs in land plants. The comprehensive study of Zf-BEDs inGossypiumsp., (cotton) also demonstrated a clear footprint of polyploidization. Overall, this comprehensive evolutionary study of Zf-BEDs in land plants highlighted significant diversity among plant species. 

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. 

Duckweed (Lemnaceae) rises as a crucial model system due to its unique characteristics and wide-ranging utility. The significance of physiological research and phytoremediation highlights the intricate potential of duckweed in the current era of plant biology. Special attention to duckweed has been brought due to its distinctive features of nutrient uptake, ion transport dynamics, detoxification, intricate signaling, and stress tolerance. In addition, duckweed can alleviate environmental pollutants and enhance sustainability by participating in bioremediation processes and wastewater treatment. Furthermore, insights into the genomic complexity of Lemnaceae species and the flourishing field of transgenic development highlight the opportunities for genetic manipulation and biotechnological innovations. Novel methods for the germplasm conservation of duckweed can be adopted to preserve genetic diversity for future research endeavors and breeding programs. This review centers around prospects in duckweed research promoting interdisciplinary collaborations and technological advancements to drive its full potential as a model organism. 

To identify sets of genes that exhibit similar expression characteristics, co-expression networks were constructed from transcriptome datasets that were obtained from plant samples at various stages of growth and development or treated with diverse biotic, abiotic, and other environmental stresses. In addition, co-expression network analysis can provide deeper insights into gene regulation when combined with transcriptomics. The coordination and integration of all these complex networks to deduce gene regulation are major challenges for plant biologists. Python and R have emerged as major tools for managing complex scientific data over the past decade. In this study, we describe a reproducible protocol POTFUL (pant co-expression transcription factor regulators), implemented in Python 3, for integrating co-expression and transcription factor target protein networks to infer gene regulation.