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Xanthomonas genes that are common in the plant-associated bacteria, but not present in reference genomes
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This review deals with a comparative analysis of seven genome sequences from plant-associated bacteria. These are the genomes of Agrobacterium tumefaciens, Mesorhizobium loti, Sinorhizobium meliloti, Xanthomonas campestris pv campestris, Xanthomonas axonopodis pv citri, Xylella fastidiosa, and Ralstonia solanacearum. Genome structure and the metabo...
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Context 1
... final list contains only those genes that did not result in a significant BLASTP hit (threshold e-value is 10 −05 ) against these genomes. Table 4 presents the list. One interesting feature of the genes listed in Table 4 is that most of them code for proteins that are located in or involved in the synthesis of the bacterial membrane or cell wall, which is to be expected from proteins important in bacterium-plant interactions. ...
Context 2
... 4 presents the list. One interesting feature of the genes listed in Table 4 is that most of them code for proteins that are located in or involved in the synthesis of the bacterial membrane or cell wall, which is to be expected from proteins important in bacterium-plant interactions. Some function in membrane transport, such as a putative iron-binding ...
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Citations
... X. fastidiosa produces biofilm and secretes several virulence factors such as cell wall-degrading enzymes (CWDEs) and lipases/esterases, among others [22][23][24]. X. fastidiosa does not have the type III secretion system (T3SS), which in most bacterial pathogens is responsible for the delivery of effectors/virulence factors inside host cells [25][26][27], thus reflecting the lifestyle of this phytopathogen that colonizes xylem vessels, a tissue that consists mostly of dead lignified cells [28]. ...
... Temecula, California, EUA [27,40] ∆rpfF -- [41] Paraburkholderia phytofirmans PsJN Allium cepa Ontario, Canada [42,43] X. fastidiosa was grown in a PD3 medium (starch 2 g/L; Soytone 2 g/L; tryptone 4 g/L; sodium citrate 1 g/L; succinate 1 g/L; hemin chloride 10 mg/L; MgSO 4 7H 2 O 1 g/L; KH 2 PO 4 1 g/L; K 2 HPO 4 1.5 g/L) for 7 days. The WT and ∆rpfF strains were maintained in a PD3 agar medium. ...
... Specifically, all surveyed amino acids (both nEAAs and EAAs) exhibited connections with high reciprocity scores (≥2), i.e., compounds and annotated genes are both linked to the same reactions or metabolic pathways from the consulted databases RheA [65] or MetaCyc [66]. CDS coding for amino acid metabolism was previously annotated in the genomes of X. fastidiosa [27] and P. phytofirmans [43]. Results for AIB showed a high reciprocity score with 18 and 11 genes in X. fastidiosa and P. phytofirmans, respectively (Supplementary Tables S4-S7). ...
Microbial competition within plant tissues affects invading pathogens’ fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce’s disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography–mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
... X. fastidiosa produces biofilm and secretes several virulence factors such as cell wall degrading enzymes (CWDE), and lipases/esterases, among others [22][23][24]. X. fastidiosa does not have the Type 3 Secretion System (T3SS), which in most bacterial pathogens is responsible for the delivery of effectors/virulence factors inside host cells [25][26][27], thus reflecting the lifestyle of this phytopathogen that colonizes xylem vessels, consisted mostly tissue consists mostly of dead lignified cells [28]. ...
... Temecula, California, EUA [27,40] ΔrpfF -- [41] Paraburkholderia phytofirmans PsJN Allium cepa Ontario, Canada [42,43] X. fastidiosa was grown in PD3 medium (2 g/L starch; soytone 2 g/L; tryptone 4 g/L; 1 g/L sodium citrate; succinate 1 g/L; 10 mg/L hemin chloride; MgSO4 .7H2O 1 g/L; KH2PO4 1 g/L; K2HPO4 1.5 g/L) for 7 days. The WT and ΔrpfF strains were maintained in a PD3-agar medium. ...
... Specifically, all surveyed amino acids (both nEAA and EAA) exhibited connections with high reciprocity scores (≥2), i.e., compounds and annotated genes are both linked to the same reactions or metabolic pathways from the consulted databases RheA [65] or MetaCyc [66]. CDS coding for amino acid metabolism was previously annotated in the genomes of X. fastidiosa [27] and P. phytofirmans [43]. Results for AIB showed a high reciprocity score with 18 and 11 genes in X. fastidiosa and P. phytofirmans, respectively (Supplementary Tables S4-S7). ...
Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall degrading enzymes, adhesion proteins, and quorum sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. LC-MS and MAGI were used to detect and map metabolites to genomes revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of a functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-Aminoisobutyric acid and Gibberellic Acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
... X. fastidiosa produces biofilm and secretes several virulence factors such as cell wall degrading enzymes (CWDE), and lipases/esterases, among others [22][23][24]. X. fastidiosa does not have the Type 3 Secretion System (T3SS), which in most bacterial pathogens is responsible for the delivery of effectors/virulence factors inside host cells [25][26][27], thus reflecting the lifestyle of this phytopathogen that colonizes xylem vessels, consisted mostly tissue consists mostly of dead lignified cells [28]. ...
... Temecula, California, EUA [27,40] ΔrpfF -- [41] Paraburkholderia phytofirmans PsJN Allium cepa Ontario, Canada [42,43] X. fastidiosa was grown in PD3 medium (2 g/L starch; soytone 2 g/L; tryptone 4 g/L; 1 g/L sodium citrate; succinate 1 g/L; 10 mg/L hemin chloride; MgSO4 .7H2O 1 g/L; KH2PO4 1 g/L; K2HPO4 1.5 g/L) for 7 days. The WT and ΔrpfF strains were maintained in a PD3-agar medium. ...
... Specifically, all surveyed amino acids (both nEAA and EAA) exhibited connections with high reciprocity scores (≥2), i.e., compounds and annotated genes are both linked to the same reactions or metabolic pathways from the consulted databases RheA [65] or MetaCyc [66]. CDS coding for amino acid metabolism was previously annotated in the genomes of X. fastidiosa [27] and P. phytofirmans [43]. Results for AIB showed a high reciprocity score with 18 and 11 genes in X. fastidiosa and P. phytofirmans, respectively (Supplementary Tables S4-S7). ...
Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall degrading enzymes, adhesion proteins, and quorum sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. LC-MS and MAGI were used to detect and map metabolites to genomes revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of a functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-Aminoisobutyric acid and Gibberellic Acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
... Increased peroxidase (PO) has been observed in several resistant interactions involving plant pathogenic fungi, bacteria, and viruses [52]. The PO activities are linked to lignification and generation of hydrogen peroxides at later stages of infection, which inhibit the pathogens directly, or the generation of other free radicals with antimicrobial effects [53,54] that restrict the development of challenging phytopathogenic bacteria [55]. Phenylalanine ammonia-lyase plays a vital role in the biosynthesis of phenolic phytoalexins [56], and during the initial establishment phase of a pathogen within the host tissues, the PAL activity often increases. ...
Background
Secretome analysis is a valuable tool to study host-pathogen protein interactions and to identify new proteins that are important for plant health. Microbial signatures elicit defense responses in plants, and by that, the plant immune system gets triggered prior to pathogen infection. Functional properties of secretory proteins from Xanthomonas axonopodis pv. dieffenbachiae (Xad1) involved in priming plant immunity was evaluated.
Results
In this study, the secretome of Xad1 was analyzed under host plant extract-induced conditions, and mass spectroscopic analysis of differentially expressed protein was identified as plant-defense-activating protein viz., flagellin C (FliC). The flagellin and Flg22 peptides both elicited hypersensitive reaction (HR) in non-host tobacco, activated reactive oxygen species (ROS) scavenging enzymes, and increased pathogenesis-related (PR) gene expression viz., NPR1, PR1, and down-regulation of PR2 (β-1,3-glucanase). Protein docking studies revealed the Flg22 epitope of Xad1, a 22 amino acid peptide region in FliC that recognizes plant receptor FLS2 to initiate downstream defense signaling.
Conclusion
The flagellin or the Flg22 peptide from Xad1 was efficient in eliciting an HR in tobacco via salicylic acid (SA)-mediated defense signaling that subsequently triggers systemic immune response epigenetically. The insights from this study can be used for the development of bio-based products (small PAMPs) for plant immunity and health.
... These molecules have also been detected in legumes in response to rhizobial inoculation (reviewed by Ferguson and Mathesius 2003). Interestingly, analysis of available rhizobial genomes reveals the presence of hundreds of genes homologous to the virulence factors of pathogens (Van Sluys et al. 2002). Therefore, the activation of genes involved in pathogen recognition may be one of the reasons why BRS Radiante establishes a less efficient N 2 fixation. ...
The common bean (Phaseolus vulgaris L.) can supply part of its N demand through biological nitrogen fixation (BNF) in symbiosis with rhizobia. However, the responses to inoculation and BNF's contribution to plant nutrition vary with the plant genotype. Here, we examined the proteome of two common bean genotypes (Ouro Negro and BRS Radiante) to determine shifts in leaf metabolism with two N sources: mineral N and inoculation with Rhizobium tropici CIAT899 (= SEMIA 4077 = BR 322). Data are available via ProteomeXchange with the identifier PXD034817. Through UPLC-MS/MS analysis, we identified 917 proteins, 338 of which are differentially expressed. Here we focus on the 64 and 22 proteins differentially expressed in BRS Radiante and Ouro Negro, respectively, when comparing the proteome profiles of inoculated and N-fertilized plants. Different pathways in P. vulgaris were affected positively and negatively in BRS Radiante during symbiosis: glutathione metabolism, cysteine and methionine metabolism, phenylpropanoid biosynthesis, sulfur metabolism, peroxisome pentose and glucuronate interconversions, amino sugar and nucleotide sugar metabolism, carbon metabolism, and phagosome were the identified pathways. However, only three pathways were affected in Ouro Negro: peroxisome, endocytosis, and sulfur metabolism. Ouro Negro shows a less affected metabolism, which may lead to a more successful symbiosis. Proteins related to defense response were also induced in BRS Radiante, implying that their activation in this genotype may be partially responsible for its less efficient symbiosis. It is important to consider the difference in the life cycles of the two cultivars, as Ouro Negro had more time to adapt to the symbiosis than BRS Radiante. These results provide a basis for future studies to identify and explore biochemical mechanisms of nitrogen fixation in common beans beyond the roots.
... Previous studies have shown that diverse plant-associated bacteria like Agrobacterium tumefaciens, Sinorhizobium meliloti, Mesorhizobium loti, Xanthomonas campestris pv campestris, Xanthomonas axonopodis pv citri, Xylella fastidiosa, and Ralstonia solanacearum have 19 nonhousekeeping genes in common (Van Sluys et al. 2002). The CRISPR loci and Cas gene cassette are considered nonhousekeeping in function as their deletions are not lethal (Sharma et al. 2022). ...
Clustered regularly interspaced short palindromic repeats (CRISPRs) are known to provide adaptive immunity to bacteria against invading bacteriophages. In recent years, CRISPR-based technologies have been used for creating improved plant varieties; however, the indigenous CRISPR-Cas elements of plant growth-promoting bacteria are usually neglected. These indigenous genetic cassettes have evolved over millions of years and have shaped the bacterial genome. Therefore, these genetic loci can be used to study the adaptive capability of the bacteria in the environment. This study aims to bioinformatically analyze the genomes of a common free-living nitrogen-fixing Azotobacter spp. to assess their CRISPR-Cas diversity. Strains of Azotobacter vinelandii and Azotobacter chroococcum were found to harbor a large number of spacers. The phylogeny of different Cas and Cse1 proteins revealed a close evolutionary relationship among A. chroococcum B3, A. chroococcum NCIMB 8003 locus II, and A. vinelandii DJ locus I. The secondary structure of the hairpin loop of the repeat was also analyzed, and a correlation was derived between the structural stability of the hairpin loop and the number of spacers acquired by the CRISPR loci. These findings revealed the diversity and evolution of the CRISPR sequences and Cas proteins in Azotobacter species. Although the adaptive immune system of bacteria against bacteriophage, CRISPR-Cas, has been identified in many bacteria, studies of plant growth-promoting bacteria have been neglected. These indigenous CRISPRs have shaped the genome over millions of years and their study can lead to the understanding of the genome composition of these organisms. Our results strengthen the idea of using A. chroococcum and A. vinelandii as biofertilizer strains as they possess more spacers with highly stable repeat sequences, thereby imparting them higher chance of survival against mobile genetic elements like phages and plasmids.
... The pathogen can be transferred to new growth on other citrus plants after the disease propagates in lesions and in the presence of moisture on them [64]. The genes that code for bacterial attachment and shallow structure components, protein secretion systems, poisons, and plant cell wall-degrading enzymes have all been discovered in Xcc and help it to survive and cause disease in citrus [65]. A study suggests that Xcc may use several pathways to attack its host [66]. ...
Citrus canker is a ravaging bacterial disease threatening citrus crops. Its major types are Asiatic Canker, Cancrosis B, and Cancrosis C, caused by Xanthomonas citri pv. citri (Xcc), Xanthomonas citri pv. aurantifolii pathotype-B (XauB), and pathotype-C (XauC), respectively. The bacterium enters its host through stomata and wounds, from which it invades the intercellular spaces in the apoplast. It produces erumpent corky necrotic lesions often surrounded by a chlorotic halo on the leaves, young stems, and fruits, which causes dark spots, defoliation, reduced photosynthetic rate, rupture of leaf epidermis, dieback, and premature fruit drop in severe cases. Its main pathogenicity determinant gene is pthA, whose variants are present in all citrus canker-causing pathogens. Countries where citrus canker is not endemic adopt different methods to prevent the introduction of the pathogen into the region, eradicate the pathogen, and minimize its dissemination, whereas endemic regions require an integrated management program to control the disease. The main aim of the present manuscript is to shed light on the pathogen profile, its mechanism of infection, and fruitful strategies for disease management. Although an adequate method to completely eradicate citrus canker has not been introduced so far, many new methods are under research to abate the disease.
... Several molecular methods for analyzing the population structure of a few plant pathogens have been utilized, e.g., RAPD, Rep, Eric-PCR, RFLP, plasmid profile analysis, PCR amplification, SDS-PAGE, 16S rDNA sequence [16,133,134,[136][137][138][139][140]. There are 4314 projected open reading frames (ORFs) on the single circular chromosome, which has a G1C content of 64.7% [141]. The G1C content of the two plasmids, pXAC64 (64,920 bp) and pXAC33 (33,699 bp), is 61.4 and 61.9%, respectively [132,141]. ...
... There are 4314 projected open reading frames (ORFs) on the single circular chromosome, which has a G1C content of 64.7% [141]. The G1C content of the two plasmids, pXAC64 (64,920 bp) and pXAC33 (33,699 bp), is 61.4 and 61.9%, respectively [132,141]. Pathogenicity, virulence, and ecological adaptation are involved in about 7% of XCC genes [141]. The XCC-A genome contains a large number of cell wall-degrading enzymes (CWDEs), proteases, iron receptors, genes related to energy metabolism pathways, the type 2 secretion system (T2SS), type 3 secretion system (T3SS) genes for flagella structural units, chemotactic protein genes, the xanthomonadin, and xanthan gum synthesis gene cluster (gumB to gumM), which are important in the epiphytic phase of the life cycle [142]. ...
... The G1C content of the two plasmids, pXAC64 (64,920 bp) and pXAC33 (33,699 bp), is 61.4 and 61.9%, respectively [132,141]. Pathogenicity, virulence, and ecological adaptation are involved in about 7% of XCC genes [141]. The XCC-A genome contains a large number of cell wall-degrading enzymes (CWDEs), proteases, iron receptors, genes related to energy metabolism pathways, the type 2 secretion system (T2SS), type 3 secretion system (T3SS) genes for flagella structural units, chemotactic protein genes, the xanthomonadin, and xanthan gum synthesis gene cluster (gumB to gumM), which are important in the epiphytic phase of the life cycle [142]. ...
Xanthomonas citri subsp. citri, a causative agent of the citrus canker (CC) disease, belongs to one of the essential groups of the bacterial phytopathogen family, Xanthomonadaceae. It has been a potential threat to the globally significant citrus fruit crop, which has remained under investigation for disease management and epidemiology since the 1980s. In Pakistan, the average yield of citrus is 11 t/ha, which is lower than other countries, including China, Brazil, and India, having average productions of 27, 26, and 22 tons/hectare, respectively. Citrus canker is one of the most devastating diseases, posing a significant threat to crop yield and fruit quality. To date, five distinct types (or forms) of the citrus canker have been recognized; the Asiatic (Canker A) form is most destructive and affects most citrus cultivars. Severe infection outcomes include dieback, defoliation, severely blemished fruit, premature fruit drop, and reduced fruit quality. The infection increases under humid, warm, cloudy climate, wind, and heavy rainfall. The analysis of plasmid and chromosomal DNA of X. citri subsp. citri depicted an evolutionary relationship among pathovars of Xanthomonas. The extensive study on the genome of X. citri subsp. citri has contributed to the current knowledge of plant host recognition of pathogens, host specificities, dissemination, and propagation. Regulatory programs, i.e., quarantine or exclusion, continued to be practiced, prohibiting infected citrus plant material into the existing stock. Other measures include removal of inoculums sources, resistant hosts, protective copper-containing sprays, and windbreak systems. In this review, we explored the latest trends in the areas of epidemiology, pathogenome, detection, host–pathogen interaction, biofilm formation, and management of X. citri subsp. citri.
... Plant associated microflora detoxifies the PM, which the host plant absorbs. PM activates Reactive Oxygen Species (ROS) that adversely affect bacteria, but bacteria have mechanisms to detoxify ROS toxicity [96,97]. Microorganisms have degradation pathways to degrade and reduce the phytotoxicity of pollutants. ...
... Ozone is a toxic compound to bacteria, and it is used as a bactericidal agent. Therefore the use of bacteria in detoxifying ozone is difficult [96,97]. ...
Indoor air pollution is a significant problem today because the release of various contaminants into the indoor air has created a major health threat for humans occupying indoors. Volatile Organic Compounds (VOCs) are pollutants released into the environment and persist in the atmosphere due to its low boiling point values. Various types of indoor activities, sources, and exposure to outdoor environments enhance indoor VOCs. This poor indoor air quality leads to adverse negative impacts on the people in the indoor environment. Many physical and chemical methods have been developed to remove or decompose these compounds from indoors. However, those methods are interrupted by many environmental and other factors in the indoor atmosphere, thus limit the applications. Therefore, there is a global need to develop an effective, promising, economical, and environmentally friendly alternatives to the problem. The use of the plant and associated microflora significantly impact reducing the environmental VOC gases, inorganic gases, particulate matter, and other pollutants contained in the air. Placing potted plants in indoor environments not only helps to remove indoor air pollutants but also to boost the mood, productivity, concentration, and creativity of the occupants and reduces stress, fatigue, sore throat, and cold. Plants normally uptake air pollutants through the roots and leaves, then metabolize, sequestrate, and excrete them. Plant-associated microorganisms help to degrade, detoxify, or sequestrate the pollutants, the air remediation, and promote plant growth. Further studies on the plant varieties and microorganisms help develop eco-friendly and environmentally friendly indoor air purifying sources.
... Bioinformaticians are focusing on the development of new methods for analyzing the available genomic datasets [69]. A number of strategies and tools have been developed for comparative genomics or genome-wide analysis [70][71][72]. Of these, genome-wide identification has been applied to identify the members of specific gene families of transcription factors by using the reference genomes and phylogenetic analysis of closely related species [73]. ...
Barley is the fourth most important cereal crop and has been domesticated and cultivated for more than 10,000 years. Breeding climate-smart and stress-tolerant cultivars are considered the most suitable way to accelerate barley improvement. However, the conventional breeding framework needs to be changed to facilitate genomics-based breeding of barley. The continuous progress in genomics has opened up new avenues and tools that are promising for making barley breeding more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing to delineate breeding have led to the development of more efficient barley cultivars. Genetic analysis, such as QTL mapping and GWAS studies using sequencing approaches, have led to the identification of molecular markers, genomic regions, and novel genes associated with the agronomic traits of barley. Furthermore, SNP marker technologies and haplotype-based GWAS have become the most applied methods for supporting molecular breeding in barley. The genetic information is also used for high-efficiency gene editing by means of CRISPR-Cas9 technology, the best example of which is the cv. Golden Promise. In this review, we summarize the genomic databases that have been developed for barley and explain how the genetic resources of the reference genome, the available state-of-the-art bioinformatics tools, and the most recent assembly of a barley pan-genome will boost the genomics-based breeding for barley improvement.
