Wall-associated kinases (WAKs) are receptors that bind pectin or small pectic fragments in the cell wall and play roles in cell elongation and pathogen response. In the Cannabis sativa (Cs) genome, 53 CsWAK/CsWAKL (WAK-like) protein family members were identified and characterized; their amino acid lengths and molecular weights varied from 582 to 983, and from 65.6 to 108.8 kDa, respectively. They were classified into four main groups by a phylogenetic tree. Out of the 53 identified CsWAK/CsWAKL genes, 23 CsWAK/CsWAKL genes were unevenly distributed among six chromosomes. Two pairs of genes on chromosomes 4 and 7 have undergone duplication. The number of introns and exons among CsWAK/CsWAKL genes ranged from 1 to 6 and from 2 to 7, respectively. The promoter regions of 23 CsWAKs/CsWAKLs possessed diverse cis-regulatory elements that are involved in light, development, environmental stress, and hormone responsiveness. The expression profiles indicated that our candidate genes (CsWAK1, CsWAK4, CsWAK7, CsWAKL1, and CsWAKL7) are expressed in leaf tissue. These genes exhibit different expression patterns than their homologs in other plant species. These initial findings are useful resources for further research work on the potential roles of CsWAK/CsWAKL in cellular signalling during development, environmental stress conditions, and hormone treatments.

/pdf/genome-wide-identification-and-expression-analysis-of-wall-n5o2wlm2.pdf

Genome-Wide Identification and Expression Analysis of Wall-Associated Kinase (WAK) Gene Family in Cannabis sativa L.

Introduction Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees. Methods and results Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis -elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters. Discussion Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation. 

pdf/systematic-evolution-of-bzip-transcription-factors-in-16x49zdegg.pdf

Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis

Plants encounter various stresses in their natural environments and can effectively respond to only one stress at a time. Through a complex gene network, transcription factors (TFs) such as WRKY TFs regulate a diverse array of stress responses. The clarification of the structural characteristics of WRKY proteins, along with recent advancements in molecular dynamics simulations, has shed light on the formation, stability, and interactions of DNA–protein complexes. This has provided a novel viewpoint regarding the control of WRKY TFs. The investigation of superfamilies, encompassing their historical development, diversity, and evolutionary patterns, has become feasible due to the transcriptome approach’s capacity to provide extensive and comprehensive transcripts. The significance of WRKY TFs lies in their pivotal role within several signaling cascades and regulatory networks that influence plant defense responses. The present review summarizes the functional aspects of the high-volume sequence data of WRKY TFs from different species studied to date. Moreover, a comparative analysis approach was utilized to determine the functions of the identified WRKY TFs in response to both abiotic and biotic stresses, as revealed through numerous studies on different plant species. The results of this review will be pivotal in understanding evolutionary events and the significance of WRKY TFs in the context of climate change, incorporating new scientific evidence to propose an innovative viewpoint. 

WRKY Transcription Factors (TFs) as Key Regulators of Plant Resilience to Environmental Stresses: Current Perspective

Cannabinoids are vital metabolites produced by Cannabis sativa. The growing market demand for cannabinoids has made C. sativa a prominent research focus. The biosynthetic pathway of cannabinoids has been extensively investigated, but the information on the transcription factors (TFs) involved in cannabinoids biosynthesis remains limited. In this study, a total of 48 CsWRKYS were identified in high-cannabidiol (CBD) hemp using a combination of two-way blast, plantTFDB prediction, and CDD batching methods. These CsWRKYs exhibited uneven distribution across ten chromosomes, and encoded 162–728 amino acids. Phylogenetic analysis revealed that CsWRKY genes were categorized into three groups, with group Ⅱ further divided into five subgroups. Members within each subfamily exhibited similar conserved motifs and exon-intron structures. Furthermore, gene expression analysis in various tissues, accompanied by cis-regulatory elements analysis, and alternative splicing analysis, provided insight into the potential roles of CsWRKYs in hemp growth and development. Notably, the expression of group III CsWRKY genes (CsWRKY1/2/20/26/28) was induced by salt, drought, and cold stress treatments. Metabolic analysis revealed an increase in the contents of cannabinoids under these treatments. Furthermore, CsWRKY20 and CsWRKY28 were proved to be positive regulatory factors of cannabinoids biosynthesis pathway. Altogether, the results of this study significantly contributes to understand the function of WRKY genes in response to abiotic stress, and their involvement in the transcriptional regulation of cannabinoid biosynthesis in high-CBD hemp. 

Genome-wide analysis of WRKY gene family in high-CBD hemp (Cannabis sativa L.) and identification of the WRKY genes involved in abiotic stress responses and regulation cannabinoid accumulation

Abstract Dioecy in flowering plants has evolved independently many different times, and thus the genetic mechanisms underlying sex determination are diverse. In hemp (Cannabis sativa), sex is controlled by a pair of sex chromosomes (XX for females and XY for males). In an attempt to understand the molecular mechanism responsible for sex expression in hemp plants, we carried out RNA-Seq of male and female plants at different developmental stages. Using a pipeline involving differential gene expression analysis and weighted gene co-expression network analysis, we identified genes important for male and female flower development. We also demonstrate that sex-biased expression is already established at very early vegetative stages, before the onset of reproductive development, and several genes encoding transcription factors of the REM, bZIP and MADS family as candidate sex determination genes in hemp. Our findings demonstrate that the gene regulatory networks governing male and female development in hemp diverge already at a very early stage, leading to profound morphological differences in male and female hemp plants. 

Identification of genes associated with sex expression and sex determination in hemp (Cannabis sativa L.)

Background: The bZIP gene family plays roles in biotic and abiotic stress, secondary metabolism, and other aspects in plants. They have been reported in Arabidopsis thaliana, Oryza sativa, Artemisia annua, and other plants, but their roles in Cannabis sativa have not been determined. Materials and Methods: In this study, we analyzed the genome-wide identification and expression profile of the bZIP gene family in C. sativa. Results: A total of 51 members of the bZIP gene family were identified based on the C. sativa genome and numbered in order from CsbZIP1 to CsbZIP51. Their phylogenetic relationships, cis-elements in promoter region, gene structures and motif compositions, physicochemical properties, chromosome locations, and expression profiles, were analyzed. The results showed that the 51 CsbZIPs were unevenly distributed on 10 chromosomes and could be clustered into 11 subfamilies. Furthermore, CsbZIPs located in the same subfamilies presented similar intron/exon organization and motif composition. The expression levels of CsbZIPs in various tissues (flowers, bracts, vegetative leaves, stems, and seeds) were determined using reverse transcription quantitative polymerase chain reaction. The expression levels of CsbZIPs were higher in flowers and bracts. The 51 CsbZIPs were explored, and their structure, evolution, and expression pattern in different tissues of C. sativa were characterized synthetically. The findings indicated that CsbZIPs are essential for the growth and development of C. sativa. Conclusions: These results provide a theoretical basis for subsequent research on hemp bZIP transcription factors and the cultivation of high-cannabidiol and low-tetrahydrocannabinol high-quality cannabis varieties.

Genome-Wide Identification and Expression Profiles of bZIP Genes in Cannabis sativa L.

Characterization and co-expression analysis of ATP-binding cassette transporters provide insight into genes related to cannabinoid transport in Cannabis sativa L.

Genomic Characterization of AP2/ERF Transcription Factors Related to Cannabinoids Biosynthesis in Cannabis Sativa L

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Genome-Wide Identification and Expression Profiles of bZIP Genes in Cannabis sativa L.

Genome-wide analysis of WRKY gene family in high-CBD hemp (Cannabis sativa L.) and identification of the WRKY genes involved in abiotic stress responses and regulation cannabinoid accumulation

Characterization and co-expression analysis of ATP-binding cassette transporters provide insight into genes related to cannabinoid transport in Cannabis sativa L.

Genomic Characterization of AP2/ERF Transcription Factors Related to Cannabinoids Biosynthesis in Cannabis Sativa L