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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.