ATP-binding cassette transporters expression profiling revealed its role in the development and regulating stress response in Solanum tuberosum.

The ATP-binding cassette (ABC) transporter gene family plays a vital role in substance transportation, including secondary metabolites, and phytohormones across membranous structures. It is still uncovered in potato (Solanum tuberosum), grown worldwide as a 3rd important food crop. The current study identified a total of 54 Stabc genes in potato genome. The accumulative phylogenetic tree of Stabc with arabidopsis, divided into eight groups (ABCA to ABCH). ABCG was the most prominent group covering 90% of Stabc genes, followed by ABCB group. The number and architecture of exon-intron varied from gene to gene. In addition, the presence of stress-responsive elements in the regulatory regions depicted their role in environmental stress. Furthermore, the tissue-specific and stress-specific expression profiling of Stabc genes and their validation through real-time-qPCR analysis revealed their role in development and stress. The presented results provided useful information for further functional analysis of Stabc genes and can also use as a reference study for other important crops.

Auxin regulated metabolic changes underlying sepal retention and development after pollination in spinach.

BACKGROUND: Pollination accelerate sepal development that enhances plant fitness by protecting seeds in female spinach. This response requires pollination signals that result in the remodeling within the sepal cells for retention and development, but the regulatory mechanism for this response is still unclear. To investigate the early pollination-induced metabolic changes in sepal, we utilize the high-throughput RNA-seq approach. RESULTS: Spinach variety 'Cornel 9' was used for differentially expressed gene analysis followed by experiments of auxin analog and auxin inhibitor treatments. We first compared the candidate transcripts expressed differentially at different time points (12H, 48H, and 96H) after pollination and detected significant difference in Trp-dependent auxin biosynthesis and auxin modulation and transduction process. Furthermore, several auxin regulatory pathways i.e. cell division, cell wall expansion, and biogenesis were activated from pollination to early developmental symptoms in sepals following pollination. To further confirm the role auxin genes play in the sepal development, auxin analog (2, 4-D; IAA) and auxin transport inhibitor (NPA) with different concentrations gradient were sprayed to the spinach unpollinated and pollinated flowers, respectively. NPA treatment resulted in auxin transport weakening that led to inhibition of sepal development at concentration 0.1 and 1 mM after pollination. 2, 4-D and IAA treatment to unpollinated flowers resulted in sepal development at lower concentration but wilting at higher concentration. CONCLUSION: We hypothesized that sepal retention and development might have associated with auxin homeostasis that regulates the sepal size by modulating associated pathways. These findings advanced the understanding of this unusual phenomenon of sepal growth instead of abscission after pollination in spinach.

Expression profiling of pathogenesis-related Protein-1 (PR-1) genes from Solanum tuberosum reveals its critical role in phytophthora infestans infection.

Pathogen-related (PR) proteins are an integral part of plants' defense mechanisms against various types of biotic and abiotic stresses. A little is known about the importance of these PR proteins in potato defense mechanisms. In the current study, a total of 22 pathogenesis-related 1 genes were identified in the potato genome. All identified proteins possessed the CAP superfamily domain with some other motifs. The cis-acting elements analysis identified several stress-responsive elements, including MYB, ABRE, and MeJRE. The gene duplication events demonstrated purifying and positive selection pressure. Expression profiling showed high transcripts level in root compared to other tissues; however, some genes have tissue-specific expression. Furthermore, the PR-1-5 gene is transcriptionally induced under Phytophthora infestans stress and hormonal (ABA and IAA) treatments. The Real-Time qPCR analysis also validated the RNA-seq data results of genes with maximum expression in roots compared to leaves and stems. The current study results provided basic data for functional characterization and can also use as a reference study for other important crops.

CRISPR/Cas9 to generate plant immunity against pathogen.

Different types of molecular approaches have been used for improving resistance against pathogens to secure food. Efficient and advanced genome editing tool as paralleled to earlier techniques like Zinc Finger Nuclease (ZFN), transcription activator-like effector nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). The approach of CRISPR/Cas9 has updated our abilities of genetic manipulation in many crops. The assembly of purposes that can be achieved through CRISPR/Cas9 and its related products make it a powerful system that will expose novel prospects in the complex domain of plant-pathogen interactions and will help to develop crop resistance against pathogens. CRISPR/Cas9 engineering permits DNA endonuclease guided by an RNA for a range of genome engineering applications across various eukaryotic species and provides an effective platform to create resistance against bacteria, viruses, insects, and fungi. In this review, we discuss CRISPR-Cas9 engineered crop plants resistant to specific pathogens.

Role of primary metabolites in plant defense against pathogens.

Plants under natural environment facing various pathogens, tend to produce defense to maintain their fitness and minimize pathogenic damage. Plant-pathogens interaction is gaining more importance by researches as, their means of the fight are primary metabolites. The ultimate result of either means of defense is pathogenesis or resistance. Plant defense mechanisms can be grouped either into inducible and constitutive defense or chemical, structural and morphological defense. Majority of defense mechanisms have a passive role, i.e. only defensive against pathogens, but a few are very active. Plant primary metabolites are catching interest in their immunity role. Deep information of molecular mechanisms involved during the plant-pathogen system is need of the day for future disease control. This review will highlight the role of primary metabolites and their mechanism of action in plant defense.

Molecular regulation of pepper innate immunity and stress tolerance: An overview of WRKY TFs.

The WRKY transcription factors (TFs) family constitutes a major group of TFs in spermatophytes. Different studies have endorsed the considerable biological roles performed by WRKY TFs in plant growth, biotic and abiotic stress responses. Genomic and transcriptomic profiling facilitate us in understanding the WRKY genes in various plants and reveal how WRKY TFs perform their action in response to different plant stresses. WRKY TFs actively take part in metabolism including carbohydrate synthesis, senescence, and secondary metabolites production. Molecular organization of WRKY TFs in plants highlight most predicted outcome of multiple responses simultaneously. Repression and activation related to W-box and other such elements is controlled at transcriptional, translational and domain level. WRKY TFs are becoming more important in crop improvement because of their binding with downstream elements. Additionally, WRKY proteins intermingle with various other TFs for modulating plant immunity. However, WRKY TFs self-regulation and crosstalk between different signaling pathways using WRKY TFs still need extensive investigations. In this review, we focused characteristics of WRKY TFs in Capsicum annum and related research advancement on their functional involvement in plant responses to the challenges of high temperature stress and pathogens infection. We summarized information about Capsicum annum WRKY TFs on the basis of their functions, their target genes and signaling pathways. Moreover, the mechanisms for synergistic responses to various biotic and abiotic stresses, WRKY target genes and other TFs as well will be of more interest with increments in existing information.

Role of secondary metabolites in plant defense against pathogens.

Pathogens get entry into host cell, reproduce there and use biological machinery of host plants which is threat to global crop production. Integrated management strategies based upon minimizing population and use of resistant cultivars can address this potential problem. In developing world farmers are less likely to adopt these approaches instead they prefer the use of chemical pesticides. Reckless use of chemical pesticides is destroying our ecosystem. That's why it is required to explore ecofriendly alternatives, like plant based metabolites to control pathogens. Studies conducted on different plant-metabolites reported that these metabolite can potentially combat plant pathogens. In this study we have also discussed some of plant secondary metabolites including alkaloids, flavonoids and phenolics. In this review we tried to highlight the new trends in utilizing secondary metabolites for controlling bacterial, viral and fungal pathogens with the hope that upcoming drugs will be human and ecosystem friendly.

Long non-coding RNAs as molecular players in plant defense against pathogens.

Long non-coding RNAs (lncRNAs) has significant role in of gene expression and silencing pathways for several biological processes in eukaryotes. lncRNAs has been reported as key player in remodeling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Host lncRNAs are reckoned as compulsory elements of plant defense. In response to pathogen attack, plants protect themselves with the help of lncRNAs -dependent immune systems in which lncRNAs regulate pathogen-associated molecular patterns (PAMPs) and other effectors. Role of lncRNAs in plant microbe interaction has been studied extensively but regulations of several lncRNAs still need extensive research. In this study we discussed and provide as overview the topical advancements and findings relevant to pathogen attack and plant defense mediated by lncRNAs. It is hoped that lncRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.

Proteomic approach to address low seed germination in Cyclobalnopsis gilva.

Seeds play essential roles in plant life cycle and germination is a complex process which is associated with different phases of water imbibition. Upon imbibition, seeds begin utilization of storage substances coupled with metabolic activity and biosynthesis of new proteins. Regeneration of organelles and emergence of radicals lead to the establishment of seedlings. All these activities are regulated in coordinated manners. Translation is the requirement of germination of seeds via involvements of several proteins like beta-amylase, starch phosphorylase. Some important proteins involved in seed germination are discussed in this review. In the past decade, several proteomic studies regarding seed germination of various species such as rice, Arabidopsis have been conducted. We face A paucity of proteomic data with respect to woody plants e.g. Fagus, Pheonix etc. With particular reference to Cyclobalnopsis gilva, a woody plant having low seed germination rate, no proteomic studies have been conducted. The review aims to reveal the complex seed germination mechanisms from woody and herbaceous plants that will help in understanding different seed germination phases and the involved proteins in C. gilva.

Tannins as antimicrobial agents: Understanding toxic effects on pathogens.

"Tannins" are compounds that belong to a group of secondary metabolites found in plants. They have a polyphenolic nature and exhibit active actions as first line defenses against invading pathogens. Several studies have demonstrated the multiple activities of tannins, highlighting their effectiveness as broad-spectrum antimicrobial agents. Tannins have reported as antibacterial, antifungal, and antiviral compounds by preventing enzymatic activities and inhibiting the synthesis of nucleic acids. Additionally, tannins primarily strengthen the plant cell wall, making it almost impenetrable to harmful pathogens. Most tannins are synthesized via the phenylpropanoid pathway to become secondary metabolites. Increased uptake of tannins has the potential to provide permanent immunity to subsequent infections by strengthening cell walls and producing antimicrobial compounds. Tannins also demonstrate a synergistic response with other defense-related molecules, such as phytoalexins and pathogenesis-related proteins, including antimicrobial peptides. Studying the mechanisms mediated by tannins on pathogen behaviors would be beneficial in stimulating plant defense against pathogens. This understanding could help explain the occurrence of diseases and outbreaks and enable potential mitigation in both natural and agricultural ecosystems.

Changes in the composition of bacterial communities and pathogen levels during wastewater treatment.

Wastewater treatment plants have been described as a potential source of spreading pathogens to the receiving water. However, few studies are reporting the presence and concentration changes of pathogens in these matrices. High-throughput sequencing provides new insights into understanding the changes of bacterial communities throughout wastewater treatment plants (WWTPs). In this study, the changes in microbial community composition and the levels of representative pathogens of effluents during the wastewater treatment process in two municipal WWTPs (A and B) were analyzed using Illumina NovaSeq sequencing and qPCR. Proteobacteria was the most abundant phylum in all samples, accounting for 45.0-75.2% of the bacterial community, followed by Firmicutes, Bacteroidetes, Actinobacteria, and Nitrospirae. A slight difference was observed between the bacterial community compositions of WWTPs A and B. However, a significant difference in the community compositions of effluent samples at different treatment stages was observed. Nutrients had a more substantial impact on bacterial community composition than physicochemical factors. Most human-associated Bacteroides and Mycobacterium were eliminated during the wastewater treatment process in both WWTPs. The bacterial community richness in WWTP A was significantly higher than that in WWTP B. The results of this study will provide insights into the potential problems that exist in WWTPs. In turn, these insights can enable the efficient and stable operation of WWTPs and help prevent the spread of pathogens.

Genome-Wide Analysis and Expression Profiling of DUF668 Genes in Glycine max under Salt Stress.

The DUF668 gene performs a critical role in mitigating the impact of abiotic stress factors. In this study, we identified 30 DUF668 genes in a soybean genome, distributed across fifteen chromosomes. The phylogenetic analysis classified the DUF668 genes into three groups (group I, group II, and group III). Interestingly, gene structure analysis illustrated that several GmDUF668 genes were without introns. Furthermore, the subcellular localization results suggested that GmDUF668 proteins were present in the nucleus, mitochondria, cytoplasm, and plasma membrane. GmDUF668 promoters were analyzed in silico to gain insight into the presence of regulatory sequences for TFs binding. The expression profiling illustrated that GmDUF668 genes showed expression in leaves, roots, nodules, and flowers. To investigate their response to salt stress, we utilized the RNA sequencing data of GmDUF668 genes. The results unveiled that GmDUF668-8, GmDUF668-20, and GmDUF668-30 genes were upregulated against salt stress treatment. We further validated these findings using qRT-PCR analysis. These findings provide a scientific basis to explore the functions of GmDUF668 genes against different stress conditions.

Post-pollination sepal longevity of female flower co-regulated by energy-associated multiple pathways in dioecious spinach.

Reproductive growth is a bioenergetic process with high energy consumption. Pollination induces female flower longevity in spinach by accelerating sepal retention and development. Cellular bioenergetics involved in cellular growth is at the foundation of all developmental activities. By contrast, how pollination alter the sepal cells bioenergetics to support energy requirement and anabolic biomass accumulation for development is less well understood. To investigate pollination-induced energy-associated pathway changes in sepal tissues after pollination, we utilized RNA-sequencing to identify transcripts that were differentially expressed between unpollinated (UNP) and pollinated flower sepals at 12, 48, and 96HAP. In total, over 6756 non-redundant DEGs were identified followed by pairwise comparisons (i.e. UNP vs 12HAP, UNP vs 48HAP, and UNP vs 96HAP). KEGG enrichment showed that the central carbon metabolic pathway was significantly activated after pollination and governed by pivotal energy-associated regulation pathways such as glycolysis, the citric acid cycle, oxidative phosphorylation, photosynthesis, and pentose phosphate pathways. Co-expression networks confirmed the synergistically regulation interactions among these pathways. Gene expression changes in these pathways were not observed after fertilization at 12HAP, but started after fertilization at 48HAP, and significant changes in gene expression occurred at 96HAP when there is considerable sepal development. These results were also supported by qPCR validation. Our results suggest that multiple energy-associated pathways may play a pivotal regulatory role in post-pollination sepal longevity for developing the seed coat, and proposed an energy pathway model regulating sepal retention in spinach.

Isolation, Identification, and Biocontrol Potential of Entomopathogenic Nematodes and Associated Bacteria against Virachola livia (Lepidoptera: Lycaenidae) and Ectomyelois ceratoniae (Lepidoptera: Pyralidae).

Virachola livia (Lepidoptera: Lycaenidae) and Ectomyelois ceratoniae (Lepidoptera: Pyralidae) are the key pests of pomegranates in Saudi Arabia that are managed mainly using broad-spectrum pesticides. Interactions between the entomopathogenic nematodes (EPNs) Steinernematids, and Heterorhabditids, and their entomopathogenic bacterial symbionts (EPBs) have long been considered monoxenic 2-partner associations responsible for killing insects and, therefore, are widely used in insect pest biocontrol. However, there are limited reports identifying such organisms in Taif, Saudi Arabia. The current study aimed to identify the EPNs and their associated bacteria isolated from Taif, Saudi Arabia, and evaluate their biocontrol potential on third instar larvae of V. livia and E. ceratoniae under laboratory conditions. A total of 35 EPN isolates belonging to Steinernema (20) and Heterorhabditis (15) were recovered from 320 soil samples. Twenty-six isolates of symbiotic or associated bacteria were isolated from EPNs and molecularly identified as Xenorhabdus (6 isolates), Photorhabdus (4 isolates), Pseudomonas (7), or Stenotrophomonas (9). A pathogenicity assay revealed that Steinernema spp. were more virulent than Heterorhabditis spp. against the two pomegranate insects, with LC50 values of 18.5 and 13.6 infective juveniles (IJs)/larva of V. livia for Steinernema spp. and 52 and 32.4 IJs/larva of V. livia for Heterorhabditis spp. at 48 and 72 h post-treatment, respectively. Moreover, LC50 values of 9 and 6.6 IJs/larva (Steinernema spp.) and 34.4 and 26.6 IJs/larva (Heterorhabditis spp.) were recorded for E. ceratoniae larvae at 48 and 72 h post-treatment. In addition, the EPB Stenotrophomonas maltophilia CQ1, isolated from Steinernema spp., surpassed Pseudomonas mosselii SJ10, associated with Heterorhabditis spp., in their ability to kill V. livia or E. ceratoniae larvae within 6 h post-application, resulting in 100% mortality in both insects after 24 and 48 h of exposure. We conclude that either application of EPNs' IJs or their associated EPBs could serve as potential biocontrol agents for V. livia and E. ceratoniae.

A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants.

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

Corrigendum: Genome-Wide Identification and Expression Profiling of Germin-Like Proteins Reveal Their Role in Regulating Abiotic Stress Response in Potato.

[This corrects the article DOI: 10.3389/fpls.2021.831140.].

Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H2O2) Under Abiotic Stress Condition.

Superoxide dismutase (SOD) proteins are important antioxidant enzymes that help plants to grow, develop, and respond to a variety of abiotic stressors. SOD gene family has been identified in a number of plant species but not yet in Daucus carota. A total of 9 DcSOD genes, comprising 2 FeSODs, 2 MnSODs, and 5 Cu/ZnSODs, are identified in the complete genome of D. carota, which are dispersed in five out of nine chromosomes. Based on phylogenetic analysis, SOD proteins from D. carota were categorized into two main classes (Cu/ZnSODs and MnFeSODs). It was predicted that members of the same subgroups have the same subcellular location. The phylogenetic analysis was further validated by sequence motifs, exon-intron structure, and 3D protein structures, with each subgroup having a similar gene and protein structure. Cis-regulatory elements responsive to abiotic stresses were identified in the promoter region, which may contribute to their differential expression. Based on RNA-seq data, tissue-specific expression revealed that DcCSD2 had higher expression in both xylem and phloem. Moreover, DcCSD2 was differentially expressed in dark stress. All SOD genes were subjected to qPCR analysis after cold, heat, salt, or drought stress imposition. SODs are antioxidants and play a critical role in removing reactive oxygen species (ROS), including hydrogen peroxide (H2O2). DcSODs were docked with H2O2 to evaluate their binding. The findings of this study will serve as a basis for further functional insights into the DcSOD gene family.

Genome wide study of cysteine rich receptor like proteins in Gossypium sp.

Cysteine-rich receptor-like-kinases (CRKs), a transmembrane subfamily of receptor-like kinase, play crucial roles in plant adaptation. As such cotton is the major source of fiber for the textile industry, but environmental stresses are limiting its growth and production. Here, we have performed a deep computational analysis of CRKs in five Gossypium species, including G. arboreum (60 genes), G. raimondii (74 genes), G. herbaceum (65 genes), G. hirsutum (118 genes), and G. barbadense (120 genes). All identified CRKs were classified into 11 major classes and 43 subclasses with the finding of several novel CRK-associated domains including ALMT, FUSC_2, Cript, FYVE, and Pkinase. Of these, DUF26_DUF26_Pkinase_Tyr was common and had elevated expression under different biotic and abiotic stresses. Moreover, the 35 land plants comparison identified several new CRKs domain-architectures. Likewise, several SNPs and InDels were observed in CLCuD resistant G. hirsutum. The miRNA target side prediction and their expression profiling in different tissues predicted miR172 as a major CRK regulating miR. The expression profiling of CRKs identified multiple clusters with co-expression under certain stress conditions. The expression analysis under CLCuD highlighted the role of GhCRK057, GhCRK059, GhCRK058, and GhCRK081 in resistant accession. Overall, these results provided primary data for future potential functional analysis as well as a reference study for other agronomically important crops.

Identification and environment-friendly biocontrol potential of five different bacteria against Aphis punicae and Aphis illinoisensis (Hemiptera: Aphididae).

The current work is aimed at isolating and identifying new Entomopathogenic bacterium (EPB) strains associated with Steinernema feltiae and assessing the EPB's biocontrol potential on Aphis punicae and Aphis illinoisensis adults in the laboratory. From S. feltiae, five bacterial isolates were isolated and molecularly characterized. Lysinibacillus xylanilyticus strain TU-2, Lysinibacillus xylanilyticus strain BN-13, Serratia liquefaciens strain TU-6, Stenotrophomonas tumulicola strain T5916-2-1b, and Pseudochrobactrum saccharolyticum strain CCUG are the strains. Pathogenicity tests demonstrated that bacterial cells were more toxic against the two aphid species than bacterial cell-free supernatants. S. tumulicola strain T5916-2-1b cells and filtrate were reported to have the strongest potential to kill A. punicae and A. illinoisensis individuals within 6 h after treatment, with 100% mortality of both insects 24 and 48 h after treatment. Based on the results of the study, it looked like endogenous Steinernema-associated EPB could be used directly as a biocontrol agent for A. punicae and A. illinoisensis.

Genome-wide comparison and identification of myosin gene family in Arabidopsis thaliana and Helianthus annuus.

Myosins are essential components of organelle trafficking in all the eukaryotic cells. Myosin driven movement plays a vital role in the development of pollen tubes, root hairs and root tips of flowering plants. The present research characterized the myosin genes in Arabidopsis thaliana and Helianthus annuus by using different computational tools. We discovered a total of 50 myosin genes and their splice variants in both pant species. Phylogenetic analysis indicated that myosin genes were divided into four subclasses. Chromosomal location revealed that myosin genes were located on all five chromosomes in A. thaliana, whereas they were present on nine chromosomes in H. annuus. Conserved motifs showed that conserved regions were closely similar within subgroups. Gene structure analysis showed that Atmyosin2.2 and Atmyosin2.3 had the highest number of introns/exons. Gene ontology analysis indicated that myosin genes were involved in vesicle transport along actin filament and cytoskeleton trafficking. Expression analysis showed that expression of myosin genes was higher during the flowering stage as compared to the seedling and budding stages. Tissue specific expression indicated that HanMYOSIN11.2, HanMYOSIN16.2 were highly expressed in stamen, whereas HanMYOSIN 2.2, HanMYOSIN 12.1 and HanMYOSIN 17.1 showed higher expression in nectary. This study enhance our understanding the function of myosins in plant development, and forms the basis for future research about the comparative genomics of plant myosin in other crop plants.