Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress

Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development

The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.

Genome-wide characterization of RR gene family members in Zanthoxylum armatum and the subsequent functional characterization of the C-type RR

Response Regulators (RRs) are crucial regulators in plant development and stress responses, comprising A-type, B-type, C-type, and pseudo-RR subfamilies. However, previous studies have often focused on specific subfamilies, which restricts our understanding of the complete RR gene family. In this study, we conducted a comprehensive analysis of 63 RR members from Zanthoxylum armatum, using phylogenetic relationships, motif composition, cis-acting elements, gene duplication and collinearity analyses. Segmental repeats among ZaRR genes enhanced the various environmental adaptabilities of Z. armatum, and the B-type ZaRR exhibited significant collinearity with the RRs in P. trichocarpa and C. sinensis. Cis-element analysis indicated ZaRRs play a significant role in abiotic stress and phytohormone pathways, particularly in light, drought, cold, abscisic acid (ABA) and salicylic acid (SA) responses. Abundant Ethylene Response Factor (ERF) and reproduction-associated binding sites in ZaRR promoters suggested their roles in stress and reproductive processes. A-type ZaRRs were implicated in plant vegetative and reproductive growth, whereas B-type ZaRRs contributed to both growth and stress responses. C-type ZaRRs were associated with plant reproductive growth, whereas pseudo-RRs may function in plant stress responses, such as water logging, cold, and response to ethylene (ETH), SA, and jasmonic acid (JA). Ectopic expression of ZaRR24, a C-type RR, inhibits growth, induces early flowering, and shortens fruit length in Arabidopsis. ZaRR24 overexpression also affected the expression of A- and B-type RRs, as well as floral meristem and organ identity genes. These findings establish a solid and comprehensive foundation for RR gene research in Z. armatum, and provide a platform for investigating signal transduction in other woody plants.

Overexpression of AcWRKY31 Increases Sensitivity to Salt and Drought and Improves Tolerance to Mealybugs in Pineapple

Pineapple is a globally significant tropical fruit, but its cultivation faces numerous challenges due to abiotic and biotic stresses, affecting its quality and quantity. WRKY transcription factors are known regulators of stress responses, however, their specific functions in pineapple are not fully understood. This study investigates the role of AcWRKY31 by overexpressing it in pineapple and Arabidopsis. Transgenic pineapple lines were obtained using Agrobacterium-mediated transformation methods and abiotic and biotic stress treatments. Transgenic AcWRKY31-OE pineapple plants showed an increased sensitivity to salt and drought stress and an increased resistance to biotic stress from pineapple mealybugs compared to that of WT plants. Similar experiments in AcWRKY31-OE, AtWRKY53-OE, and the Arabidopsis Atwrky53 mutant were performed and consistently confirmed these findings. A comparative transcriptomic analysis revealed 5357 upregulated genes in AcWRKY31-OE pineapple, with 30 genes related to disease and pathogen response. Notably, 18 of these genes contained a W-box sequence in their promoter region. A KEGG analysis of RNA-Seq data showed that upregulated DEG genes are mostly involved in translation, protein kinases, peptidases and inhibitors, membrane trafficking, folding, sorting, and degradation, while the downregulated genes are involved in metabolism, protein families, signaling, and cellular processes. RT-qPCR assays of selected genes confirmed the transcriptomic results. In summary, the AcWRKY31 gene is promising for the improvement of stress responses in pineapple, and it could be a valuable tool for plant breeders to develop stress-tolerant crops in the future.

Genome-wide identification, expression analysis of WRKY transcription factors in Citrus ichangensis and functional validation of CiWRKY31 in response to cold stress

BACKGROUND

Ichang papeda (Citrus ichangensis), a wild perennial plant of the Rutaceae family, is a cold-hardy plant. WRKY transcription factors are crucial regulators of plant growth and development as well as abiotic stress responses. However, the WRKY genes in C. ichangensis (CiWRKY) and their expression patterns under cold stress have not been thoroughly investigated, hindering our understanding of their role in cold tolerance.

RESULTS

In this study, a total of 52 CiWRKY genes identified in the genome of C. ichangensis were classified into three main groups and five subgroups based on phylogenetic analysis. Comprehensive analyses of motif features, conserved domains, and gene structures were performed. Segmental duplication plays a significant role in the CiWRKY gene family expansion. Cis-acting element analysis revealed the presence of various stress-responsive elements in the promoters of the majority of CiWRKYs. Gene ontology (GO) analysis and protein-protein interaction predictions indicate that the CiWRKYs exhibit crucial roles in regulation of both development and stress response. Expression profiling analysis demonstrates that 14 CiWRKYs were substantially induced under cold stress. Virus-induced gene silencing (VIGS) assay confirmed that CiWRKY31, one of the cold-induced WRKYs, functions positively in regulation of cold tolerance.

CONCLUSION

Sequence and protein properties of CiWRKYs were systematically analyzed. Among the 52 CiWRKY genes 14 members exhibited cold-responsive expression patterns, and CiWRKY31 was verified to be a positive regulator of cold tolerance. These findings pave way for future investigations to understand the molecular functions of CiWRKYs in cold tolerance and contribute to unravelling WRKYs that may be used for engineering cold tolerance in citrus.

Genome-wide identification, characterization, and evolutionary analysis of the barley TALE gene family and its expression profiles in response to exogenous hormones

Three-amino-loop-extension (TALE) family belongs to the homeobox gene superfamily and occurs widely in plants, playing a crucial role in regulating their growth and development. Currently, genome-wide analysis of the TALE family has been completed in many plants. However, the systematic identification and hormone response analysis of the TALE gene family in barley are still lacking. In this study, 21 TALE candidate genes were identified in barley, which can be divided into KNOX and BELL subfamilies. Barley TALE members in the same subfamily of the phylogenetic tree have analogically conserved motifs and gene structures, and segmental duplications are largely responsible for the expansion of the HvTALE family. Analysis of TALE orthologous and homologous gene pairs indicated that the HvTALE family has mainly undergone purifying selective pressure. Through spatial structure simulation, HvKNOX5-HvKNOX6 and HvKNOX5-HvBELL11 complexes are all formed through hydrogen bonding sites on both the KNOX2 and homeodomain (HD) domains of HvKNOX5, which may be essential for protein interactions among the HvTALE family members. Expression pattern analyses reveal the potential involvement of most HvTALE genes in responses to exogenous hormones. These results will lay the foundation for regulation and function analyses of the barley TALE gene family in plant growth and development by hormone regulation.

The WRKY gene family in the halophyte Limonium bicolor: identification, expression analysis, and regulation of salt stress tolerance

KEY MESSAGE

63 L. bicolor WRKY genes were identified and their informatics was analyzed. The results suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Salt stress, as a universal abiotic stress, severely inhibits the growth and development of plants. WRKY transcription factors play a vital role in plant growth and development, as well as in response to various stresses. Nevertheless, little is known of systematic genome-wide analysis of the WRKY genes in Limonium bicolor, a model recretohalophyte. In this study, 63 L. bicolor WRKY genes were identified (LbWRKY1-63), which were unevenly distributed across seven chromosomes and one scaffold. Based on the structural and phylogenetic characteristics, 63 LbWRKYs are divided into three main groups. Cis-elements in the LbWRKY promoters were related to growth and development, phytohormone responses, and stress responses. Colinearity analysis showed strong colinearity between LbWRKYs and GmWRKYs from soybean (Glycine max). Therefore, LbWRKY genes maybe have similar functions to GmWRKY genes. Expression analysis showed that 28 LbWRKY genes are highly expressed in roots, 9 in stems, 26 in leaves, and 12 in flowers and most LbWRKY genes responded to NaCl, ABA, and PEG6000. Silencing LbWRKY10 reduced salt gland density and salt secretion ability of leaves, and the salt tolerance of the species. Consistent with this, genes associated with salt gland development were markedly down-regulated in the LbWRKY10-silenced lines. Our findings suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Our research provides new insights into the functions of the WRKY family in halophytes.

Genome-Wide Identification and Expression Analysis of the High-Mobility Group B (HMGB) Gene Family in Plant Response to Abiotic Stress in Tomato

High-mobility group B (HMGB) proteins are a class of non-histone proteins associated with eukaryotic chromatin and are known to regulate a variety of biological processes in plants. However, the functions of HMGB genes in tomato (Solanum lycopersicum) remain largely unexplored. Here, we identified 11 members of the HMGB family in tomato using BLAST. We employed genome-wide identification, gene structure analysis, domain conservation analysis, cis-acting element analysis, collinearity analysis, and qRT-PCR-based expression analysis to study these 11 genes. These genes were categorized into four groups based on their unique protein domain structures. Despite their structural diversity, all members contain the HMG-box domain, a characteristic feature of the HMG superfamily. Syntenic analysis suggested that tomato SlHMGBs have close evolutionary relationships with their homologs in other dicots. The promoter regions of SlHMGBs are enriched with numerous cis-elements related to plant growth and development, phytohormone responsiveness, and stress responsiveness. Furthermore, SlHMGB members exhibited distinct tissue-specific expression profiles, suggesting their potential roles in regulating various aspects of plant growth and development. Most SlHMGB genes respond to a variety of abiotic stresses, including salt, drought, heat, and cold. For instance, SlHMGB2 and SlHMGB4 showed positive responses to salt, drought, and cold stresses. SlHMGB1, SlHMGB3, and SlHMGB8 were involved in responses to two types of stress: SlHMGB1 responded to drought and heat, while SlHMGB3 and SlHMGB8 responded to salt and heat. SlHMGB6 and SlHMGB11 were solely regulated by drought and heat stress, respectively. Under various treatment conditions, the number of up-regulated genes significantly outnumbered the down-regulated genes, implying that the SlHMGB family may play a crucial role in mitigating abiotic stress in tomato. These findings lay a foundation for further dissecting the precise roles of SlHMGB genes.

Genome-wide identification of nitrate transporter 1/peptide transporter family (NPF) induced by arbuscular mycorrhiza in the maize genome

The Transporter 1/Peptide Transporter Family (NPF) is essential for the uptake and transport of nitrate nitrogen. Significant increases in nitrogen have been increasingly reported for many mycorrhizal plants, but there are few reports on maize. Here, we have identified the maize NPF family and screened for arbuscular mycorrhiza fungi (AMF) induced NPFs. In this study, a systematic analysis of the maize NPF gene family was performed. A total of 82 NPF genes were identified in maize. ZmNPF4.5 was strongly induced by AMF in both low and high nitrogen. Lotus japonicus hairy root-induced transformation experiments showed that ZmNPF4.5 promoter-driven GUS activity was restricted to cells containing tufts. Yeast backfill experiments indicate that ZmNPF4.5 functions in nitrate uptake. Therefore, we speculate that ZmNPF4.5 is a key gene for nitrate-nitrogen uptake in maize through the mycorrhizal pathway. This is a reference value for further exploring the acquisition of nitrate-nitrogen by maize through AMF pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01464-3.

Genome-wide identification, expression analysis, and abiotic stress response of the CBL and CIPK gene families in Artocarpus nanchuanensis

Artocarpus nanchuanensis, the northernmost species in the jackfruit genus, has great economic and horticultural value due to its nutritious fruit and beautiful tree shape. Calcineurin B-like proteins (CBLs) act as plant-specific Ca2+ sensors and participate in regulating plant responses to various abiotic stresses by interacting with CBL-interacting protein kinases (CIPKs). However, the characteristics and functions of the CBL and CIPK genes in A. nanchuanensis are still unclear. Here, we identified 14 CBL and 33 CIPK genes from the A. nanchuanensis genome, and based on phylogenetic analysis, they were divided into 4 and 7 clades, respectively. Gene structure and motif analysis indicated that the AnCBL and AnCIPK genes were relatively conserved. Colinear analysis showed that segmental duplication contributed to the expansion of the AnCBL and AnCIPK gene families. Expression analysis showed that AnCBL and AnCIPK genes were widely expressed in various tissues of A. nanchuanensis and exhibited tissue-specific expression. In addition, three genes (AnCBL6, AnCIPK7/8) may play important roles in response to salt, cold, and drought stresses. In summary, this study lays an important foundation for the improvement of stress resistance in A. nanchuanensis and provides new insight for the functional research on CBL and CIPK gene families.

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.

SlWRKY80-mediated jasmonic acid pathway positively regulates tomato resistance to saline-alkali stress by enhancing spermidine content and stabilizing Na+/K+ homeostasis

Saline-alkali is an important abiotic stressor influencing tomato production. Exogenous methyl jasmonate (MeJA) is well known to increase tomato resistance to a variety of stresses, although its exact mechanism is yet unknown. In this study we confirmed that 22.5 μmol/l MeJA could significantly improve the saline-alkali stress resistance of tomato. Saline-alkali (300 mM) stress increased the endogenous MeJA and jasmonic acid (JA) contents of tomato by 18.8 and 13.4%, respectively. Exogenous application of 22.5 μmol/l MeJA increased the endogenous MeJA and JA contents in tomato by 15.2 and 15.9%, respectively. Furthermore, we found an important transcription factor, SlWRKY80, which responded to MeJA, and constructed its overexpressing and knockout lines through genetic transformation. It was found that SlWRKY80 actively regulated tomato resistance to saline-alkali stress, and the spraying of exogenous MeJA (22.5 μmol/l) reduced the sensitivity of SlWRKY80 knockout lines to saline-alkali stress. The SlWRKY80 protein directly combines with the promoter of SlSPDS2 and SlNHX4 to positively regulate the transcription of SlSPDS2 and SlNHX4, thereby promoting the synthesis of spermidine and Na+/K+ homeostasis, actively regulating saline-alkali stress. The augmentation of JA content led to a notable reduction of 70.6% in the expression of SlJAZ1, and the release of the SlWRKY80 protein interacting with SlJAZ1. In conclusion, we revealed the mechanism of exogenous MeJA in tomato stress resistance through multiple metabolic pathways, elucidated that exogenous MeJA further promotes spermidine synthesis and Na+/K+ homeostasis by activating the expression of SlWRKY80, which provides a new theoretical basis for the study of the JA stress resistance mechanism and the production of tomato.

Genome-wide identification and characterization of FAD family genes in barley

Fatty acid desaturases (FADs) play pivotal roles in determining plant stress tolerance. Barley is the most salt-tolerant cereal crop. In this study, we performed genome-wide identification and characterization analysis of the FAD gene family in barley (Hordeum vulgare). A total of 24 HvFADs were identified and divided into four subfamilies based on their amino acid sequence similarity. HvFADs unevenly distributed on six of seven barley chromosomes, and three clusters of HvFADs mainly occurred on the chromosome 2, 3 and 6. Segmental duplication events were found to be a main cause for the HvFAD gene family expansion. The same HvFAD subfamily showed the relatively consistent exon-intron composition and conserved motifs of HvFADs. Cis-element analysis in HvFAD promoters indicated that the expression of HvFADs may be subject to complex regulation, especially stress-responsive elements that may involve in saline-alkaline stress response. Combined transcriptomic data with quantitative experiments, at least five HvFADs highly expressed in roots under salt or alkali treatment, suggesting they may participate in saline or alkaline tolerance in barley. This study provides novel and valuable insights for underlying salt/alkali-tolerant mechanisms in barley.

Identification and characterization of the Remorin gene family in Saccharum and the involvement of ScREM1.5e-1/-2 in SCMV infection on sugarcane

Introduction

Remorins (REMs) are plant-specific membrane-associated proteins that play important roles in plant-pathogen interactions and environmental adaptations. Group I REMs are extensively involved in virus infection. However, little is known about the REM gene family in sugarcane (Saccharum spp. hyrid), the most important sugar and energy crop around world.

Methods

Comparative genomics were employed to analyze the REM gene family in Saccharum spontaneum. Transcriptomics or RT-qPCR were used to analyze their expression files in different development stages or tissues under different treatments. Yeast two hybrid, bimolecular fluorescence complementation and co-immunoprecipitation assays were applied to investigate the protein interaction.

Results

In this study, 65 REMs were identified from Saccharum spontaneum genome and classified into six groups based on phylogenetic tree analysis. These REMs contain multiple cis-elements associated with growth, development, hormone and stress response. Expression profiling revealed that among different SsREMs with variable expression levels in different developmental stages or different tissues. A pair of alleles, ScREM1.5e-1/-2, were isolated from the sugarcane cultivar ROC22. ScREM1.5e-1/-2 were highly expressed in leaves, with the former expressed at significantly higher levels than the latter. Their expression was induced by treatment with H2O2, ABA, ethylene, brassinosteroid, SA or MeJA, and varied upon Sugarcane mosaic virus (SCMV) infection. ScREM1.5e-1 was localized to the plasma membrane (PM), while ScREM1.5e-2 was localized to the cytoplasm or nucleus. ScREM1.5e-1/-2 can self-interact and interact with each other, and interact with VPgs from SCMV, Sorghum mosaic virus, or Sugarcane streak mosaic virus. The interactions with VPgs relocated ScREM1.5e-1 from the PM to the cytoplasm.

Discussion

These results reveal the origin, distribution and evolution of the REM gene family in sugarcane and may shed light on engineering sugarcane resistance against sugarcane mosaic pathogens.

Review: Structural-functional relationship of WRKY transcription factors: Unfolding the role of WRKY in plants

WRKY as the name suggests, are the transcription factors (TFs) that contain the signature WRKY domains, hence named after it. Since their discovery in 1994, they have been well studied in plants with exploration of approximately 74 WRKY genes in the model plant, Arabidopsis alone. However, the study of these transcription factors (TFs) is not just limited to model plant now. They have been studied widely in crop plants as well, because of their tremendous contribution in stress as well as in growth and development. Here, in this review, we describe the story of WRKY TFs from their identification to their origin, the binding mechanisms, structure and their contribution in regulating plant development and stress physiology. High throughput transcriptomics-based data also opened a doorway to understand the comprehensive and detailed functioning of WRKY TFs in plants. Indeed, the detailed functional role of each and every WRKY member in regulating the gene expression is required to pave the path to develop holistic understanding of their role in stress physiology and developmental processes in plants.

Genome-wide identification and expression profiling of the WRKY gene family reveals abiotic stress response mechanisms in Platycodon grandiflorus

The WRKY family of transcription factors (TFs) is an important gene family involved in abiotic stress responses. Although the roles of WRKY TFs in plant abiotic stress responses are well studied, little is known about the stress-induced changes in WRKY family in Platycodon grandiflorus. 42 PgWRKY genes in seven subgroups were identified in the P. grandiflorus genome. The content of eight platycodins in P. grandiflorus was investigated under cold, heat, and drought stresses. Platycodin D levels significantly increased under three abiotic stresses, while the content changes of other platycodins varied. Transcriptome analysis showed that different WRKY family members exhibited varied expression patterns under different abiotic stresses. PgWRKY20, PgWRKY26, and PgWRKY39 were identified as three key candidates for temperature and drought stress responses, and were cloned and analysed for sequence characteristics, gene structure, subcellular localisation, and expression patterns. The RT-qPCR results showed that PgWRKY26 expression significantly increased after heat stress for 48 h, cold stress for 6 h, and drought stress for 2 d (DS_2 d). The PgWRKY39 expression level significantly increased at DS_2 d. This study provides a theoretical basis for clarifying the molecular mechanism of the abiotic stress responses of the WRKY gene family in P. grandiflorus.

Boron homeostasis affects Longan yield: a study of NIP and BOR boron transporter of two cultivars

BACKGROUND

Essential micronutrient Boron (B) plays crucial roles in plant survival and reproduction but becomes toxic in higher quantities. Although plant cells have different B transport systems, B homeostasis is mainly maintained by two transporter protein families: B exporters (BOR) and nodulin-26-like intrinsic proteins (NIP). Their diversity and differential expression are responsible for varied B tolerance among plant varieties and species. Longan is a highly admired subtropical fruit with a rising market in China and beyond. In the present study, we cultured Shixia (SX) and Yiduo (YD), two differently characterized Longan cultivars, with foliar B spray. We analyzed their leaf physiology, fruit setting, B content, and boron transporter gene expression of various tissue samples. We also traced some of these genes' subcellular localization and overexpression effects.

RESULTS

YD and SX foliage share similar microstructures, except the mesophyll cell wall thickness is double in YD. The B spray differently influenced their cellular constituents and growth regulators. Gene expression analysis showed reduced BOR genes expression and NIP genes differential spatiotemporal expression. Using green fluorescent protein, two high-expressing NIPs, NIP1 and NIP19, were found to translocate in the transformed tobacco leaves' cell membrane. NIPs transformation of SX pollen was confirmed using magnetic beads and quantified using a fluorescence microscope and polymerase chain reaction. An increased seed-setting rate was observed when YD was pollinated using these pollens. Between the DlNIP1 and DlNIP19 transformed SX pollen, the former germinated better with increasing B concentrations and, compared to naturally pollinated plants, had a better seed-setting rate in YD♀ × SX♂.

CONCLUSION

SX and YD Longan have different cell wall structures and react differently to foliar B spray, indicating distinct B tolerance and management. Two B transporter NIP genes were traced to localize in the plasma membrane. However, under high B concentrations, their differential expression resulted in differences in Jasmonic acid content, leading to differences in germination rate. Pollination of YD using these NIPs transformed SX pollen also showed NIP1 overexpression might overcome the unilateral cross incompatibility between YD♀ × SX♂ and can be used to increase Longan production.

Genome-wide identification and characterization of the RZFP gene family and analysis of its expression pattern under stress in Populus trichocarpa

Forest trees face many abiotic stressors during their lifetime, including drought, heavy metals, high salinity, and chills, affecting their quality and yield. The RING-type ubiquitin ligase E3 is an invaluable component of the ubiquitin-proteasome system (UPS) and participates in plant growth and environmental interactions. Interestingly, only a few studies have explored the RING ZINC FINGER PROTEIN (RZFP) gene family. This study identified eight PtrRZFPs genes in the Populus genome, and their molecular features were analyzed. Gene structure analysis revealed that all PtrRZFPs genes contained >10 introns. Evolutionarily, the RZFPs were separated into four categories, and segmental replication events facilitated their amplification. Notably, many stress-related elements have been identified in the promoters of PtrRZFPs using Cis-acting element analysis. Moreover, some PtrRZFPs were significantly induced by drought and sorbitol, revealing their potential roles in regulating stress responses. Particularly, overexpression of the PtrRZFP1 gene in poplars conferred excellent drought tolerance; however, PtrRZFP1 knockdown plants were drought-sensitive. We identified the potential upstream transcription factors of PtrRZFPs and revealed the possible biological functions of RZFP1/4/7 in resisting osmotic and salt stress, laying the foundation for subsequent biological function studies and providing genetic resources for genetic engineering breeding for drought resistance in forest trees. This study offers crucial information for the further exploration of the functions of RZFPs in poplars.

Genome-wide identification and expression analysis of WRKY gene family members in red clover (Trifolium pratense L.)

Trifolium pratense is an important legume forage grass and a key component of sustainable livestock development. Serving as an essential component, the WRKY gene family, a crucial group of regulatory transcription factors in plants, holds significant importance in their response to abiotic stresses. However, there has been no systematic analysis conducted on the WRKY gene family in Trifolium pratense. This study conducted a comprehensive genomic characterization of the WRKY gene family in Trifolium pratense, utilizing the latest genomic data, resulting in the identification of 59 TpWRKY genes. Based on their structural features, phylogenetic characteristics, and conserved motif composition, the WRKY proteins were classified into three groups, with group II further subdivided into five subgroups (II-a, II-b, II-c, II-d, and II-e). The majority of the TpWRKYs in a group share a similar structure and motif composition. Intra-group syntenic analysis revealed eight pairs of duplicate segments. The expression patterns of 59 TpWRKY genes in roots, stems, leaves, and flowers were examined by analyzing RNA-seq data. The expression of 12 TpWRKY genes under drought, low-temperature (4°C), methyl jasmonate (MeJA) and abscisic acid (ABA) stresses was analyzed by RT-qPCR. The findings indicated that TpWRKY46 was highly induced by drought stress, and TpWRKY26 and TpWRKY41 were significantly induced by low temperature stress. In addition, TpWRKY29 and TpWRKY36 were greatly induced by MeJA stress treatment, and TpWRKY17 was significantly upregulated by ABA stress treatment. In this research, we identified and comprehensively analyzed the structural features of the WRKY gene family in T.pratense, along with determined the possible roles of WRKY candidate genes in abiotic stress. These discoveries deepen our understandings of how WRKY transcription factors contribute to species evolution and functional divergence, laying a solid molecular foundation for future exploration and study of stress resistance mechanisms in T.pratense.

Genome-wide identification, expression analysis, and functional study of the bZIP transcription factor family and its response to hormone treatments in pea (Pisum sativum L.)

BACKGROUND

Basic leucine zipper (bZIP) protein is a plant-specific transcription factor involved in various biological processes, including light signaling, seed maturation, flower development, cell elongation, seed accumulation protein, and abiotic and biological stress responses. However, little is known about the pea bZIP family.

RESULTS

In this study, we identified 87 bZIP genes in pea, named PsbZIP1 ~ PsbZIP87, via homology analysis using Arabidopsis. The genes were divided into 12 subfamilies and distributed unevenly in 7 pea chromosomes. PsbZIPs in the same subfamily contained similar intron/exon organization and motif composition. 1 tandem repeat event and 12 segmental duplication events regulated the expansion of the PsbZIP gene family. To better understand the evolution of the PsbZIP gene family, we conducted collinearity analysis using Arabidopsis thaliana, Oryza sativa Japonica, Fagopyrum tataricum, Solanum lycopersicum, Vitis vinifera, and Brachypodium distachyon as the related species of pea. In addition, interactions between PsbZIP proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of PsbZIP expression was complex. We also evaluated the expression patterns of bZIP genes in different tissues and at different fruit development stages, all while subjecting them to five hormonal treatments.

CONCLUSION

These results provide a deeper understanding of PsbZIP gene family evolution and resources for the molecular breeding of pea. The findings suggested that PsbZIP genes, specifically PSbZIP49, play key roles in the development of peas and their response to various hormones.

Genome-wide identification and characterization of GRAS gene family in pigeonpea (Cajanus cajan (L.) Millspaugh)

The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03782-x.

Genome-Wide Identification and Characterization of the WRKY Gene Family in Cucurbita maxima

In higher plants, WRKY transcription factors are broadly involved in a variety of life activities and play an important role in both biotic and abiotic stress responses. However, little is known about the functions of WRKY genes in the popular species, such as Cucurbita maxima (pumpkin), which is planted worldwide. In the present study, 102 CmWRKY genes were identified in the C. maxima genome. Chromosome location, multiple sequence alignment, phylogenetic analysis, and synteny analysis of the CmWRKYs were performed. Notably, we found that silencing CmWRKY22 promoted cucumber mosaic virus (CMV) infection, whereas overexpression of CmWRKY22 inhibited the CMV infection. Subsequently, an electrophoretic mobility shift assay (EMSA) confirmed that CmWRKY22 was able to bind to the W-box at the promoter of CmPR1b, which is a responsive gene of the salicylic acid (SA) signaling pathway. In summary, this study has provided a foundation for the antiviral functions of WRKY transcription factors in C. maxima.

Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut (Arachis hypogaea L.)

Cytochrome P450s (CYPs) constitute extensive enzyme superfamilies in the plants, playing pivotal roles in a multitude of biosynthetic and detoxification pathways essential for growth and development, such as the flavonoid biosynthesis pathway. However, CYPs have not yet been systematically studied in the cultivated peanuts (Arachis hypogaea L.), a globally significant cash crop. This study addresses this knowledge deficit through a comprehensive genome-wide analysis, leading to the identification of 589 AhCYP genes in peanuts. Through phylogenetic analysis, all AhCYPs were systematically classified into 9 clans, 43 gene families. The variability in the number of gene family members suggests specialization in biological functions. Intriguingly, both tandem duplication and fragment duplication events have emerged as pivotal drivers in the evolutionary expansion of the AhCYP superfamily. Ka/Ks analysis underscored the substantial influence of strong purifying selection on the evolution of AhCYPs. Furthermore, we selected 21 genes encoding 8 enzymes associated with the flavonoid pathway. The results of quantitative real-time PCR (qRT-PCR) experiments unveiled stage-specific expression patterns during the development of peanut testa, with discernible variations between pink and red testa. Importantly, we identified a direct correlation between gene expression levels and the accumulation of metabolites. These findings offer valuable insights into elucidating the comprehensive functions of AhCYPs and the underlying mechanisms governing the divergent accumulation of flavonoids in testa of different colors.

Genome-Wide Characterization of the Maize (Zea mays L.) WRKY Transcription Factor Family and Their Responses to Ustilago maydis

Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens.

Genome-Wide Identification and Analysis of WRKY Gene Family in Melastoma dodecandrum

WRKY is one of the largest transcription factor families in plants and plays an important role in plant growth and development as well as in abiotic and biological stresses. However, there is little information about the WRKY family in Melastoma dodecandrum. In this study, 126 WRKY members were identified in M. dodecandrum. According to phylogenetic analysis, they were divided into three major groups, and group II was further divided into five subgroups. MedWRKY genes were unevenly distributed on 12 chromosomes. Additionally, the gene structure and sequence composition were similar within the same group and differed between groups, suggesting their functional diversity. The promoter sequence analysis identified a number of cis-acting elements related to plant growth and development, stress response, and secondary metabolite synthesis in the WRKY gene family. The collinearity analysis showed that gene replication events were the main driving force of MedWRKY gene evolution. The transcriptome data and RT-qPCR analysis suggested that MedWRKY genes had higher expression in the roots and ripe fruit of M. dodecandrum. In short, this paper lays a foundation for further study of the functions and molecular mechanism of M. dodecandrum WRKY gene family.

Identification of tomato AHL gene families and functional analysis their roles in fruit development and abiotic stress response

The AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) transcription factors play important roles in regulating plant development and stress response. However, the AHL family genes have not been identified in tomato (Solanum lycopersicum) and their biological functions have not been elucidated. In this work, the gene families encoding AHLs were identified in tomato genome, and their physical and chemical characteristics, subcellular localization, gene expression profiles during fruit development and upon abiotic stimulus were investigated. Overall, a total of 18 AHL members were identified in tomato genome, phylogenetic analysis classified these SlAHL members into two clades, clade A (SlAHL1-8) and clade B (SlAHL9-18). Six clade A SlAHLs were detected to be subcellular localized in the nucleus. The transcripts of the representative clade A SlAHLs predominantly accumulated 10 days post anthesis (dpa) in tomato fruits, revealing an involvement of these SlAHLs in early fruit development. Furthermore, compared with clade B members, the transcripts of the clade A SlAHLs were more responsive to heat, drought, cold and salt stresses, suggesting that these SlAHLs may play major roles in response to abiotic stresses. Moreover, overexpression of SlAHL1 and SlAHL7 in Arabidopsis increased the sensitivity to ABA during seed germination and seedling stages. Overexpression of SlAHL1 inhibited seed germination while increased primary root elongation upon salt and drought stresses. Together, our work suggested that the clade A SlAHL genes may play an important role in response to abiotic stresses, which paving the way for future functional analysis of AHL genes in tomato and other Solanaceae species.

Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis

In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.

Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover

Background

White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover.

Methods and Results

In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress.

Conclusion

The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.

bHLH transcription factor family identification, phylogeny, and its response to abiotic stress in Chenopodium quinoa

The second-largest transcription factor superfamily in plants is that of the basic helix-loop-helix (bHLH) family, which plays an important complex physiological role in plant growth, tissue development, and environmental adaptation. Systematic research on the Chenopodium quinoa bHLH family will enable a better understanding of this species. Herein, authors used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 218 CqbHLH genes identified. A total of 218 CqbHLH transcription factor genes were identified in the whole genome, located on 18 chromosomes. A phylogenetic tree was constructed using the CqbHLH and AtbHLH proteins to determine their homology, and the members were divided into 20 subgroups and one unclustered gene. Authors also analyzed 218 CqbHLH genes, conservative motifs, chromosome diffusion, and gene replication. The author constructed one Neighbor-Joining (NJ) tree and a collinearity analysis map of the bHLH family in C. quinoa and six other plant species to study the evolutionary relationship and homology among multiple species. In addition, the expression levels of 20 CqbHLH members from different subgroups in various tissues, different fruit developmental stages, and six abiotic stresses were analyzed. Authors identified 218 CqbHLH genes and studied their biological functions, providing a basis for better understanding and further studying the bHLH family in quinoa.

Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica

BACKGROUND

WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKY genes (PsWRKY) remains lacking.

RESULTS

This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions.

CONCLUSIONS

Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.

Genome-Wide Investigation of BAM Gene Family in Annona atemoya: Evolution and Expression Network Profiles during Fruit Ripening

β-amylase proteins (BAM) are important to many aspects of physiological process such as starch degradation. However, little information was available about the BAM genes in Annona atemoya, an important tropical fruit. Seven BAM genes containing the conservative domain of glycoside hydrolase family 14 (PF01373) were identified with Annona atemoya genome, and these BAM genes can be divided into four groups. Subcellular localization analysis revealed that AaBAM3 and AaBAM9 were located in the chloroplast, and AaBAM1.2 was located in the cell membrane and the chloroplast. The AaBAMs belonging to Subfamily I contribute to starch degradation have the higher expression than those belonging to Subfamily II. The analysis of the expression showed that AaBAM3 may function in the whole fruit ripening process, and AaBAM1.2 may be important to starch degradation in other organs. Temperature and ethylene affect the expression of major AaBAM genes in Subfamily I during fruit ripening. These expressions and subcellular localization results indicating β-amylase play an important role in starch degradation.

The genome of Acorus deciphers insights into early monocot evolution

Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.

Genome-Wide Identification, Characterization and Expression Analysis of Plant Nuclear Factor (NF-Y) Gene Family Transcription Factors in Saccharum spp

Plant nuclear factor (NF-Y) is a transcriptional activating factor composed of three subfamilies: NF-YA, NF-YB, and NF-YC. These transcriptional factors are reported to function as activators, suppressors, and regulators under different developmental and stress conditions in plants. However, there is a lack of systematic research on the NF-Y gene subfamily in sugarcane. In this study, 51 NF-Y genes (ShNF-Y), composed of 9 NF-YA, 18 NF-YB, and 24 NF-YC genes, were identified in sugarcane (Saccharum spp.). Chromosomal distribution analysis of ShNF-Ys in a Saccharum hybrid located the NF-Y genes on all 10 chromosomes. Multiple sequence alignment (MSA) of ShNF-Y proteins revealed conservation of core functional domains. Sixteen orthologous gene pairs were identified between sugarcane and sorghum. Phylogenetic analysis of NF-Y subunits of sugarcane, sorghum, and Arabidopsis showed that ShNF-YA subunits were equidistant while ShNF-YB and ShNF-YC subunits clustered distinctly, forming closely related and divergent groups. Expression profiling under drought treatment showed that NF-Y gene members were involved in drought tolerance in a Saccharum hybrid and its drought-tolerant wild relative, Erianthus arundinaceus. ShNF-YA5 and ShNF-YB2 genes had significantly higher expression in the root and leaf tissues of both plant species. Similarly, ShNF-YC9 had elevated expression in the leaf and root of E. arundinaceus and in the leaf of a Saccharum hybrid. These results provide valuable genetic resources for further sugarcane crop improvement programs.

Genome-wide identification and bioinformatics analysis of the WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea (Rhododendron simsii)

WRKY transcription factors have been demonstrated to influence the anthocyanin biosynthesis in many plant species. However, there is limited knowledge about the structure and function of WRKY genes in the major ornamental plant azalea (Rhododendron simsii). In this study, we identified 57 RsWRKY genes in the R. simsii genome and classified them into three main groups and several subgroups based on their structural and phylogenetic characteristics. Comparative genomic analysis suggested WRKY gene family has significantly expanded during plant evolution from lower to higher species. Gene duplication analysis indicated that the expansion of the RsWRKY gene family was primarily due to whole-genome duplication (WGD). Additionally, selective pressure analysis (Ka/Ks) suggested that all RsWRKY duplication gene pairs underwent purifying selection. Synteny analysis indicated that 63 and 24 pairs of RsWRKY genes were orthologous to Arabidopsis thaliana and Oryza sativa, respectively. Furthermore, RNA-seq data was used to investigate the expression patterns of RsWRKYs, revealing that 17 and 9 candidate genes may be associated with anthocyanin synthesis at the bud and full bloom stages, respectively. These findings provide valuable insights into the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species and lay the foundation for future functional studies of WRKY genes.

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Neolamarckia cadamba

The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a 'miracle tree' for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba.

Nanoparticles-Based Delivery Systems for Salicylic Acid as Plant Growth Stimulator and Stress Alleviation

The population growth tendency leads to an increase in demand for food products, and in particular, products obtained from the processing of plants. However, there are issues of biotic and abiotic stresses that can significantly reduce crop yields and escalate the food crisis. Therefore, in recent years, the development of new methods of plant protection became an important task. One of the most promising ways to protect plants is to treat them with various phytohormones. Salicylic acid (SA) is one of the regulators of systemic acquired resistance (SAR) signaling pathways. These mechanisms are able to protect plants from biotic and abiotic stresses by increasing the expression of genes that encode antioxidant enzymes. However, salicylic acid in high doses can act as an antagonist and have the negative rebound effect of inhibition of plant growth and development. To maintain optimal SA concentrations in the long term, it is necessary to develop systems for the delivery and slow release of SA in plants. The purpose of this review is to summarize and study methods of delivery and controlled release of SA in a plant. Various carriers-based nanoparticles (NPs) synthesized from both organic and inorganic compounds, their chemical structure, impacts on plants, advantages, and disadvantages are comprehensively discussed. The mechanisms of controlled release of SA and the effects of the use of the considered composites on the growth and development of plants are also described. The present review will be helpful to design or fabricate NPs and NPs-based delivery systems for salicylic acid-controlled release and better understating of the mechanism of SA-NPs interaction to alleviate stress on plants.

LcWRKY17, a WRKY Transcription Factor from Litsea cubeba, Effectively Promotes Monoterpene Synthesis

The WRKY gene family is one of the most significant transcription factor (TF) families in higher plants and participates in many secondary metabolic processes in plants. Litsea cubeba (Lour.) Person is an important woody oil plant that is high in terpenoids. However, no studies have been conducted to investigate the WRKY TFs that regulate the synthesis of terpene in L. cubeba. This paper provides a comprehensive genomic analysis of the LcWRKYs. In the L. cubeba genome, 64 LcWRKY genes were discovered. According to a comparative phylogenetic study with Arabidopsis thaliana, these L. cubeba WRKYs were divided into three groups. Some LcWRKY genes may have arisen from gene duplication, but the majority of LcWRKY evolution has been driven by segmental duplication events. Based on transcriptome data, a consistent expression pattern of LcWRKY17 and terpene synthase LcTPS42 was found at different stages of L. cubeba fruit development. Furthermore, the function of LcWRKY17 was verified by subcellular localization and transient overexpression, and overexpression of LcWRKY17 promotes monoterpene synthesis. Meanwhile, dual-Luciferase and yeast one-hybrid (Y1H) experiments showed that the LcWRKY17 transcription factor binds to W-box motifs of LcTPS42 and enhances its transcription. In conclusion, this research provided a fundamental framework for future functional analysis of the WRKY gene families, as well as breeding improvement and the regulation of secondary metabolism in L. cubeba.

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

Identification of CNGCs in Glycine max and Screening of Related Resistance Genes after Fusarium solani Infection

Cyclic nucleotide-gated channels (CNGCs), non-selective cation channels localised on the plasmalemma, are involved in growth, development, and regulatory mechanisms in plants during adverse stress. To date, CNGC gene families in multiple crops have been identified and analysed. However, there have been no systematic studies on the evolution and development of CNGC gene families in legumes. Therefore, in the present study, via transcriptome analysis, we identified 143 CNGC genes in legumes, and thereafter, classified and named them according to the grouping method used for Arabidopsis thaliana. Functional verification for disease stress showed that four GmCNGCs were specifically expressed in the plasmalemma during the stress process. Further, functional enrichment analysis showed that their mode of participation and coordination included inorganic ion concentration regulation inside and outside the membrane via the transmembrane ion channel and participation in stress regulation via signal transduction. The CNGC family genes in G. max involved in disease stress were also identified and physiological stress response and omics analyses were also performed. Our preliminary results revealed the basic laws governing the involvement of CNGCs in disease resistance in G. max, providing important gene resources and a theoretical reference for the breeding of resistant soybean.

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

Characterization and functional analyses of wheat TaPR1 genes in response to stripe rust fungal infection

The pathogenesis-related protein-1 (PR1) gene is important for plants to respond to various biotic and abiotic stresses. Unlike those in model plants, PR1 genes in wheat have not been systematically studied. Herein, we identified 86 potential TaPR1 wheat genes using bioinformatics tools and RNA sequencing. Kyoto Encyclopedia of Genes and Genomes analysis indicated that the TaPR1 genes were involved in the salicylic acid signalling pathway, MAPK signalling pathway, and phenylalanine metabolism in response to Pst-CYR34 infection. Ten of the TaPR1 genes were structurally characterized and validated by RT‒PCR. One particular gene, TaPR1-7, was found to be associated with resistance to Puccinia striiformis f. sp. tritici (Pst) in a biparental wheat population. Virus-induced gene silencing showed that TaPR1-7 is important for Pst resistance in wheat. This study provides the first comprehensive study on wheat PR1 genes, improving our overall understanding of these genes in plant defenses, particularly against stripe rust.

Identification of histone acetyltransferase genes responsible for cannabinoid synthesis in hemp

BACKGROUND

Histone acetyltransferases (HATs) play an important role in plant growth and development, stress response, and regulation of secondary metabolite biosynthesis. Hemp (Cannabis sativa L.) is famous for its high industrial, nutritional, and medicinal value. It contains non-psychoactive cannabinoid cannabidiol (CBD) and cannabinol (CBG), which play important roles as anti-inflammatory and anti-anxiety. At present, the involvement of HATs in the regulation of cannabinoid CBD and CBG synthesis has not been clarified.

METHODS

The members of HAT genes family in hemp were systematically analyzed by bioinformatics analysis. In addition, the expression level of HATs and the level of histone acetylation modification were analyzed based on transcriptome data and protein modification data. Real-time quantitative PCR was used to verify the changes in gene expression levels after inhibitor treatment. The changes of CBD and CBG contents after inhibitor treatment were verified by HPLC-MS analysis.

RESULTS

Here, 11 HAT genes were identified in the hemp genome. Phylogenetic analysis showed that hemp HAT family genes can be divided into six groups. Cannabinoid synthesis genes exhibited spatiotemporal specificity, and histones were acetylated in different inflorescence developmental stages. The expression of cannabinoid synthesis genes was inhibited and the content of CBD and CBG declined by 10% to 55% in the samples treated by HAT inhibitor (PU139). Results indicated that CsHAT genes may regulate cannabinoid synthesis through altering histone acetylation.

CONCLUSIONS

Our study provides genetic information of HATs responsible for cannabinoid synthesis, and offers a new approach for increasing the content of cannabinoid in hemp.

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

Characterization of the WRKY Gene Family Related to Anthocyanin Biosynthesis and the Regulation Mechanism under Drought Stress and Methyl Jasmonate Treatment in Lycoris radiata

Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and abiotic stress responses. The WRKY TF family has been identified and investigated in many medicinal plants, but its members and functions are not identified in L. radiata. In this study, a total of 31 L. radiata WRKY (LrWRKY) genes were identified based on the transcriptome-sequencing data. Next, the LrWRKYs were divided into three major clades (Group I-III) based on the WRKY domains. A motif analysis showed the members within same group shared a similar motif component, indicating a conservational function. Furthermore, subcellular localization analysis exhibited that most LrWRKYs were localized in the nucleus. The expression pattern of the LrWRKY genes differed across tissues and might be important for Lycoris growth and flower development. There were large differences among the LrWRKYs based on the transcriptional levels under drought stress and MeJA treatments. Moreover, a total of 18 anthocyanin components were characterized using an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis and pelargonidin-3-O-glucoside-5-O-arabinoside as well as cyanidin-3-O-sambubioside were identified as the major anthocyanin aglycones responsible for the coloration of the red petals in L. radiata. We further established a gene-to-metabolite correlation network and identified LrWRKY3 and LrWRKY27 significant association with the accumulation of pelargonidin-3-O-glucoside-5-O-arabinoside in the Lycoris red petals. These results provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in anthocyanin biosynthesis and in response to drought stress and MeJA treatment.

Genome-wide identification, evolution, and expression analysis of carbonic anhydrases genes in soybean (Glycine max)

Carbonic anhydrases (CAs), as zinc metalloenzymes, are ubiquitous in nature and play essential roles in diverse biological processes. Although CAs have been broadly explored and studied, comprehensive characteristics of CA gene family members in the soybean (Glycine max) are still lacking. A total of 35 CA genes (GmCAs) were identified; they distributed on sixteen chromosomes of the soybean genome and can be divided into three subfamilies (α-type, β-type, and γ-type). Bioinformatics analysis showed that the specific GmCA gene subfamily or clade exhibited similar characteristics and that segmental duplications took the major role in generating new GmCAs. Furthermore, the synteny and evolutionary constraints analyses of CAs among soybean and distinct species provided more detailed evidence for GmCA gene family evolution. Cis-element analysis of promoter indicated that GmCAs may be responsive to abiotic stress and regulate photosynthesis. Moreover, the expression patterns of GmCAs varied in different tissues at diverse developmental stages in soybean. Additionally, we found that eight representative GmCAs may be involved in the response of soybean to low phosphorus stress. The systematic investigation of the GmCA gene family in this study will provide a valuable basis for further functional research on soybean CA genes.

Genome-wide analysis of the SBT gene family involved in drought tolerance in cotton

The subtilisin-like proteases (SBTs) are a large family of serine peptidases that are unique to plants. Previous studies have shown that SBTs are associated with developmental processes and environmental responses. However, comprehensive identification and systematic analysis of the SBT family have not been conducted in cotton. We used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structures, expression modes, evolutionary relationships, selection pressures and stress responses of SBT gene family members in upland cotton. In this study, we identified 120 and 112 SBTs in the tetraploid cotton species G. hirsutum and G. barbadense, while 67 and 69 SBTs were identified in the diploid species G. arboreum and G. raimondii, respectively; these SBTs were divided into five distinct subfamilies. We identified the SBT gene GhSBT27A, and explore its function through virus-induced gene silencing and transmission electron microscopy. These results suggested that the GhSBT27A gene was involved in the response to drought stress. These results lay a foundation for further study on the drought stress mechanism of cotton.

Responses of ABCB and ABCC transporters to the toxic dinoflagellate Prorocentrum lima in the mussel Perna viridis

Bivalve mollusks can accumulate diarrheic shellfish poisoning (DSP) toxins through filter-feeding, but they exhibit some resistance to the toxins. Previous studies have suggested that the ABC transporters may have an important role in the resistance to DSP toxins, but comprehensive studies are lacking. In this study, we comprehensively analyzed the distribution of ABC transporters in the mussel Perna viridis, and observed responses of ABCB and ABCC transporters to the DSP toxins-producing dinoflagellate Prorocentrum lima. Total 39 members of ABC transporters were identified in P. viridis, including 3 full PvABCBs, 3 half PvABCBs, and 7 PvABCCs transporters. We found that PvABCBs and PvABCCs subfamilies were expressed in hemocytes, gills and digestive gland with some difference, especially in hemocytes. After exposure to P. lima, PvABCBs and PvABCCs displayed different expression changes in different tissues. The short-term (3 h) exposure to P. lima induced the transcription of PvABCB1_like1, PvABCB6, PvABCC1, PvABCC1_like and PvABCC1/3, and the longer-term (96 h) exposure increased the transcription of PvABCB1, PvABCB1_like, PvABCB10, PvABCC1 and PvABCC1_like1 in gills and PvABCC10 in digestive gland. These results suggest that different types of PvABCBs and PvABCCs in P. viridis may contribute to the detoxification of DSP toxins in different tissues at different time after exposure to DSP toxins. Our finding provides new evidence for further understanding the role of ABC transporters in the tolerance of mussel to DSP toxins.

Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in Platycodon grandiflorus

Platycodon grandiflorus, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of P. grandiflorus are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in P. grandiflorus. In this study, 27 PgWRKYs were identified in the P. grandiflorus transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.

Genome-Wide Identification of MIKCc-Type MADS-Box Family Gene and Floral Organ Transcriptome Characterization in Ma Bamboo (Dendrocalamus latiflorus Munro)

Most bamboos die after flowering, and the molecular mechanisms responsible for flowering is poorly understood. The MIKCc-type MADS-box family gene is involved in the flowering process. To explore the mechanism of the MIKCc-type MADS-box gene and phytohormone regulation in the flowering of Dendrocalamus latiflorus Munro (D. latiflorus), characterized by extremely rapid growth and widely cultivated woody bamboo, we initially did a genome-wide analysis of the MIKCc-type MADS-box gene in D. latiflorus. In the meantime, transcriptome analysis was performed using the floral organs. A total of 170 MIKCc-Type MADS-Box genes were identified and divided into 15 categories. The cis-acting element analysis in promoters regions revealed that MIKC-type MADS-box family genes were associated with hormones, including auxin, abscisic acid (ABA), gibberellin (GA) and jasmonic acid (JA), which was found at 79, 476, 96, 486 sites and cover 61, 103, 73, 128 genes. Genome synteny analysis showed subgenome AA and BB were better than CC and obtained 49, 40, 39 synteny genes compared with Oryza sativa (O. sativa). In transcriptome analysis of floral organs, the enriched pathway from DEGs included circadian, vernalization and gibberellin pathways associated with the flowering process. We found that the jasmonic acid synthesis gene is highly expressed in the pistil, which may be the cause of Ma bamboo pollen abortion. The expression profile showed that most MIKC-type MADS-box genes exhibited high expression in flower organs. The consequences of this study will provide insight into the irregular flowering and low pollen counts of Ma bamboo.