Comprehensive Analysis of the Chitinase Gene Family in Cucumber (Cucumis sativus L.): From Gene Identification and Evolution to Expression in Response to Fusarium oxysporum

Characterization of soybean chitinase genes induced by rhizobacteria involved in the defense against Fusarium oxysporum

Rhizobacteria are capable of inducing defense responses via the expression of pathogenesis-related proteins (PR-proteins) such as chitinases, and many studies have validated the functions of plant chitinases in defense responses. Soybean (Glycine max) is an economically important crop worldwide, but the functional validation of soybean chitinase in defense responses remains limited. In this study, genome-wide characterization of soybean chitinases was conducted, and the defense contribution of three chitinases (GmChi01, GmChi02, or GmChi16) was validated in Arabidopsis transgenic lines against the soil-borne pathogen Fusarium oxysporum. Compared to the Arabidopsis Col-0 and empty vector controls, the transgenic lines with GmChi02 or GmChi16 exhibited fewer chlorosis symptoms and wilting. While GmChi02 and GmChi16 enhanced defense to F. oxysporum, GmChi02 was the only one significantly induced by Burkholderia ambifaria. The observation indicated that plant chitinases may be induced by different rhizobacteria for defense responses. The survey of 37 soybean chitinase gene expressions in response to six rhizobacteria observed diverse inducibility, where only 10 genes were significantly upregulated by at least one rhizobacterium and 9 genes did not respond to any of the rhizobacteria. Motif analysis on soybean promoters further identified not only consensus but also rhizobacterium-specific transcription factor-binding sites for the inducible chitinase genes. Collectively, these results confirmed the involvement of GmChi02 and GmChi16 in defense enhancement and highlighted the diverse inducibility of 37 soybean chitinases encountering F. oxysporum and six rhizobacteria.

Overexpression of cucumber CYP82D47 enhances resistance to powdery mildew and Fusarium oxysporum f. sp. cucumerinum

Cytochrome P450s are a large family of protein-encoding genes in plant genomes, many of which have not yet been comprehensively characterized. Here, a novel P450 gene, CYP82D47, was isolated and functionally characterized from cucumber (Cucumis sativus L.). Quantitative real-time reverse-transcription polymerase chain reaction analysis revealed that CYP82D47 expression was triggered by salicylic acid (SA) and ethephon (ETH). Expression analysis revealed a correlation between CYP82D47 transcript levels and plant defense responses against powdery mildew (PM) and Fusarium oxysporum f. sp. cucumerinum (Foc). Although no significant differences were observed in disease resistance between CYP82D47-RNAi and wild-type cucumber, overexpression (OE) of CYP82D47 enhanced PM and Foc resistance in cucumber. Furthermore, the expression levels of SA-related genes (PR1, PR2, PR4, and PR5) increased in CYP82D47-overexpressing plants 7 days post fungal inoculation. The levels of ETH-related genes (EIN3 and EBF2) were similarly upregulated. The observed enhanced resistance was associated with the upregulation of SA/ETH-signaling-dependent defense genes. These findings indicate the crucial role of CYP82D47 in pathogen defense in cucumber. CYP82D47-overexpressing cucumber plants exhibited heightened susceptibility to both diseases. The study results offer important insights that could aid in the development of disease-resistant cucumber cultivars and elucidate the molecular mechanisms associated with the functions of CYP82D47.

Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection

Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses.

Maize plant expresses SWEET transporters differently when interacting with Trichoderma asperellum and Fusarium verticillioides, two fungi with different lifestyles

Most Trichoderma species are beneficial fungi that promote plant growth and resistance, while Fusarium genera cause several crop damages. During the plant-fungi interaction there is a competition for sugars in both lifestyles. Here we analyzed the plant growth promotion and biocontrol activity of T. asperellum against F. verticillioides and the effect of both fungi on the expression of the maize diffusional sugar transporters, the SWEETs. The biocontrol activity was done in two ways, the first was by observing the growth capacity of both fungus in a dual culture. The second one by analyzing the infection symptoms, the chlorophyl content and the transcript levels of defense genes determined by qPCR in plants with different developmental stages primed with T. asperellum conidia and challenged with F. verticillioides. In a dual culture, T. asperellum showed antagonist activity against F. verticillioides. In the primed plants a delay in the infection disease was observed, they sustained chlorophyll content even after the infection, and displayed upregulated defense-related genes. Additionally, the T. asperellum primed plants had longer stems than the nonprimed plants. SWEETs transcript levels were analyzed by qPCR in plants primed with either fungus. Both fungi affect the transcript levels of several maize sugar transporters differently. T. asperellum increases the expression of six SWEETs on leaves and two at the roots and causes a higher exudation of sucrose, glucose, and fructose at the roots. On the contrary, F. verticillioides reduces the expression of the SWEETs on the leaves, and more severely when a more aggressive strain is in the plant. Our results suggest that the plant is able to recognize the lifestyle of the fungi and respond accordingly by changing the expression of several genes, including the SWEETs, to establish a new sugar flux.

Genome-Wide Identification, Expression, and Response to Fusarium Infection of the SWEET Gene Family in Garlic (Allium sativum L.)

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I-IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars.

Bioinformatics and Expression Analysis of the Chitinase Genes in Strawberry (Fragaria vesca) and Functional Study of FvChi-14

Plant chitinases (EC 3.2.1.14) are pathogenesis-related (PR) proteins and are well studied in many plant species. However, little is known about the genomic organization and expression of chitinase genes in strawberries (Fragaria vesca). Here, 23 FvChi genes were identified in the genome of strawberry (F. vesca) and divided into GH18 and GH19 subfamilies based on phylogenetic relationships. A detailed bioinformatics analysis of the FvChi genes was performed, including gene physicochemical properties, chromosomal location, exon-intron distribution, domain arrangement, and subcellular localization. Twenty-two FvChi genes showed upregulation after Colletotrichum gloeosporioides infection. Following the exogenous application of SA, FvChi-3, 4, and 5 showed significant changes in expression. The ectopic expression of FvChi-14 in Arabidopsis thaliana increased resistance to C. higginsianum via controlling the SA and JA signaling pathway genes (AtPR1, AtICS1, AtPDF1.2, and AtLOX3). The FvChi-14 protein location was predicted in the cell wall or extracellular matrix. We speculate that FvChi-14 is involved in disease resistance by regulating the SA and JA signaling pathways. The findings of this study provide a theoretical reference for the functional studies of FvChi genes and new candidates for strawberry stress resistance breeding programs.

Multifaceted production strategies and applications of glucosamine: a comprehensive review

Glucosamine (GlcN) and its derivatives are in high demand and used in various applications such as food, a precursor for the biochemical synthesis of fuels and chemicals, drug delivery, cosmetics, and supplements. The vast number of applications attributed to GlcN has raised its demand, and there is a growing emphasis on developing production methods that are sustainable and economical. Several: physical, chemical, enzymatic, microbial fermentation, recombinant processing methods, and their combinations have been reported to produce GlcN from chitin and chitosan available from different sources, such as animals, plants, and fungi. In addition, genetic manipulation of certain organisms has significantly improved the quality and yield of GlcN compared to conventional processing methods. This review will summarize the chitin and chitosan-degrading enzymes found in various organisms and the expression systems that are widely used to produce GlcN. Furthermore, new developments and methods, including genetic and metabolic engineering of Escherichia coli and Bacillus subtilis to produce high titers of GlcN and GlcNAc will be reviewed. Moreover, other sources of glucosamine production viz. starch and inorganic ammonia will also be discussed. Finally, the conversion of GlcN to fuels and chemicals using catalytic and biochemical conversion will be discussed.

Assessment of the Molecular Responses of an Ancient Angiosperm against Atypical Insect Oviposition: The Case of Hass Avocados and the Tephritid Fly Anastrepha ludens

Anastrepha spp. (Diptera: Tephritidae) infestations cause significant economic losses in commercial fruit production worldwide. However, some plants quickly counteract the insertion of eggs by females by generating neoplasia and hindering eclosion, as is the case for Persea americana Mill., cv. Hass (Hass avocados). We followed a combined transcriptomics/metabolomics approach to identify the molecular mechanisms triggered by Hass avocados to detect and react to the oviposition of the pestiferous Anastrepha ludens (Loew). We evaluated two conditions: fruit damaged using a sterile pin (pin) and fruit oviposited by A. ludens females (ovi). We evaluated both of the conditions in a time course experiment covering five sampling points: without treatment (day 0), 20 min after the treatment (day 1), and days 3, 6, and 9 after the treatment. We identified 288 differentially expressed genes related to the treatments. Oviposition (and possibly bacteria on the eggs' surface) induces a plant hypersensitive response (HR), triggering a chitin receptor, producing an oxidative burst, and synthesizing phytoalexins. We also observed a process of cell wall modification and polyphenols biosynthesis, which could lead to polymerization in the neoplastic tissue surrounding the eggs.

Genome-wide characterization of the chitinase gene family in wild apple (Malus sieversii) and domesticated apple (Malus domestica) reveals its role in resistance to Valsa mali

Chitinases are responsible for catalyzing the hydrolysis of chitin and contribute to plant defense against fungal pathogens by degrading fungal chitin. In this study, genome-wide identification of the chitinase gene family of wild apple (Malus sieversii) and domesticated apple (Malus domestica) was conducted, and the expression profile was analyzed in response to Valsa mali infection. A total of 36 and 47 chitinase genes belonging to the glycosyl hydrolase 18 (GH18) and 19 (GH19) families were identified in the genomes of M. sieversii and M. domestica, respectively. These genes were classified into five classes based on their phylogenetic relationships and conserved catalytic domains. The genes were randomly distributed on the chromosomes and exhibited expansion by tandem and segmental duplication. Eight of the 36 MsChi genes and 17 of the 47 MdChi genes were differentially expressed in response to V. mali inoculation. In particular, MsChi35 and its ortholog MdChi41, a class IV chitinase, were constitutively expressed at high levels in M. sieversii and domesticated apple, respectively, and may play a crucial role in the defense response against V. mali. These results improve knowledge of the chitinase gene family in apple species and provide a foundation for further studies of fungal disease prevention in apple.

A chitinase CsChi23 promoter polymorphism underlies cucumber resistance against Fusarium oxysporum f. sp. cucumerinum

Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), leads to widespread yield loss and quality decline in cucumber. However, the molecular mechanisms underlying Foc resistance remain poorly understood. We report the mapping and functional characterisation of CsChi23, encoding a cucumber class I chitinase with antifungal properties. We assessed sequence variations at CsChi23 and the associated defence response against Foc. We functionally characterised CsChi23 using transgenic assay and expression analysis. The mechanism regulating CsChi23 expression was assessed by genetic and molecular approaches. CsChi23 was induced by Foc infection, which led to rapid upregulation in resistant cucumber lines. Overexpressing CsChi23 enhanced fusarium wilt resistance and reduced fungal biomass accumulation, whereas silencing CsChi23 causes loss of resistance. CsHB15, a homeodomain leucine zipper (HD-Zip) III transcription factor, was found to bind to the CsChi23 promoter region and activate its expression. Furthermore, silencing of CsHB15 reduces CsChi23 expression. A single-nucleotide polymorphism variation -400 bp upstream of CsChi23 abolished the HD-Zip III binding site in a susceptible cucumber line. Collectively, our study indicates that CsChi23 is sufficient to enhance fusarium wilt resistance and reveals a novel function of an HD-Zip III transcription factor in regulating chitinase expression in cucumber defence against fusarium wilt.

Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max)

Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I–V. From a broader view, the I–V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.

What will polyethylene film mulching bring to the root-associated microbial community of Paeonia ostii?

Plastic film mulching can increase crop yield and is widely used in agricultural production, but long-term mulching could adversely affect plant growth. To investigate the related mechanism, we studied the bacterial communities in different root-associated compartments of Paeonia ostii, a perennial oil crop, under polyethylene film mulching for three years by full-length 16S rDNA sequencing technology, and measured the soil physicochemical properties and enzyme activities. We found that enzyme activities and available nutrients in the soil tended to decrease after long-term mulching. Analysis of bacterial community composition revealed that the endosphere may be another potential source of the root-associated microbiome of P. ostii, and the rhizoplane plays a selective gating role in the enrichment processes for P. ostii microbiome assembly. Long-term mulching affected the abundance of dominant bacterial communities in different root-associated compartments and reduced the bacterial richness in the endosphere, but increased bacterial interactions in each compartment, as well as between different compartments. We speculate that this is mainly related to the decrease of litter content and the serious degradation of polyethylene film after long-term mulching, which resulted in microplastics and other harmful substances entering the soil. Our study further explained the reasons for the harm of long-term film mulching on plants to guide the rational use of plastic film. KEY POINTS: •Soil enzyme activities and available nutrients decreased after long-term mulching. •Mulching affected the dominant bacterial abundance in different root-associated compartments. •Mulching increased bacterial interactions among compartments.

Research Advances in Genetic Mechanisms of Major Cucumber Diseases Resistance

Cucumber (Cucumis sativus L.) is an important economic vegetable crop worldwide that is susceptible to various common pathogens, including powdery mildew (PM), downy mildew (DM), and Fusarium wilt (FM). In cucumber breeding programs, identifying disease resistance and related molecular markers is generally a top priority. PM, DM, and FW are the major diseases of cucumber in China that cause severe yield losses and the genetic-based cucumber resistance against these diseases has been developed over the last decade. Still, the molecular mechanisms of cucumber disease resistance remain unclear. In this review, we summarize recent findings on the inheritance, molecular markers, and quantitative trait locus mapping of cucumber PM, DM, and FM resistance. In addition, several candidate genes, such as PM, DM, and FM resistance genes, with or without functional verification are reviewed. The data help to reveal the molecular mechanisms of cucumber disease resistance and provide exciting new opportunities for further resistance breeding.

Pretreatment with Chitosan Prevents Fusarium Infection and Induces the Expression of Chitinases and β-1,3-Glucanases in Garlic (Allium sativum L.)

Fusarium infection decreases the yield of garlic (Allium sativum L.); however, the knowledge about garlic response to fungal attack is limited. Chitosan induces plant defense response to stress conditions. Here, we analyzed the effects of chitosan with low (Ch1, 39 kDa) and medium (Ch2, 135 kDa) molecular weight on Fusarium infection in garlic. Ch1 and Ch2 at concentrations 0.125–0.400 mg/mL suppressed the growth of Fusarium proliferatum cultures in vitro. Pretreatment of garlic bulbs with Ch1 or Ch2 prevented disease symptoms after F. proliferatum inoculation, while exerting early inhibitory and late stimulatory effects on chitinase and β-1,3-glucanase activities. Ch1/Ch2 treatment of garlic already infected with F. proliferatum caused transcriptional upregulation of chitinases and β-1,3-glucanases at the early stage, which was maintained at the late stage in Ch2-treated samples, but not in Ch1-treated samples, where transcriptional inhibition was observed. The stimulatory effect of Ch2 pretreatment on the expression of chitinase and endo-β-1,3-glucanase genes was stronger than that of Ch1 pretreatment, suggesting that Ch2 could be more effective than Ch1 in pre-sowing treatment of garlic bulbs. Our results provide insights into the effects of chitosan on the garlic response to Fusarium, suggesting a novel strategy to protect garlic crop against fungal infection.

Characterization of the Chitinase Gene Family in Mulberry (Morus notabilis) and MnChi18 Involved in Resistance to Botrytis cinerea

Chitinase is a hydrolase that uses chitin as a substrate. It plays an important role in plant resistance to fungal pathogens by degrading chitin. Here, we conducted bioinformatics analysis and transcriptome data analysis of the mulberry (Morus notabilis) chitinase gene family to determine its role in the resistance to Botrytis cinerea. A total of 26 chitinase genes were identified, belonging to the GH18 and GH19 families. Among them, six chitinase genes were differentially expressed under the infection of B. cinerea. MnChi18, which significantly responded to B. cinerea, was heterologously expressed in Arabidopsis (Arabidopsis thaliana). The resistance of MnChi18 transgenic Arabidopsis to B. cinerea was significantly enhanced, and after inoculation with B. cinerea, the activity of catalase (CAT) increased and the content of malondialdehyde (MDA) decreased. This shows that overexpression of MnChi18 can protect cells from damage. In addition, our study also indicated that MnChi18 may be involved in B. cinerea resistance through other resistance-related genes. This study provides an important basis for further understanding the function of mulberry chitinase.

Chitinase Chi 2 Positively Regulates Cucumber Resistance against Fusarium oxysporum f. sp. cucumerinum

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), severely restricts cucumber growth and yield. Accumulating lines of evidence indicate that chitinases play important roles in attacking the invading fungal pathogens through catalyzing their cell wall degradation. Here, we identified the chitinase (Chi) genes in cucumber and further screened the FW-responsive genes via a comparative transcriptome analysis and found that six common genes were predominantly expressed in roots but also significantly upregulated after Foc infection. Expression verification further conformed that Chi2 and Chi14 were obviously induced by Foc as well as by hormone treatments, compared with the controls. The purified Chi2 and Chi14 proteins significantly affected the growth of Foc in vitro, compared with the controls. Knockdown of Chi2 in cucumber by virus-induced gene silencing (VIGS) increased susceptibility to FW, compared with the Chi14-silenced and control plants, and silencing of Chi2 drastically impaired gene activation in the jasmonic acid pathway, suggesting that the Chi2 gene might play positive roles in cucumber FW defense and, therefore, can provide a gene resource for developing cucumber-FW-resistance breeding programs.

Transcriptional responses to Fusarium oxysporum f. sp. lycopersici (Sacc.) Snyder & Hansen infection in three Colombian tomato cultivars

BACKGROUND

Fusarium oxysporum f. sp. lycopersici (Fol) is a compendium of pathogenic and non-pathogenic fungal strains. Pathogenic strains may cause vascular wilt disease and produce considerable losses in commercial tomato plots. To gain insight into the molecular mechanisms mediating resistance to Fol in tomato, the aim of our study was to characterize the transcriptional response of three cultivars (CT1, CT2 and IAC391) to a pathogenic (Fol-pt) and a non-pathogenic (Fo-npt) strain of Fo.

RESULTS

All cultivars exhibited differentially expressed genes in response to each strain of the fungus at 36 h post-inoculation. For the pathogenic strain, CT1 deployed an apparent active defense response that included upregulation of WRKY transcription factors, an extracellular chitinase, and terpenoid-related genes, among others. In IAC391, differentially expressed genes included upregulated but mostly downregulated genes. Upregulated genes mapped to ethylene regulation, pathogenesis regulation and transcription regulation, while downregulated genes potentially impacted defense responses, lipid transport and metal ion binding. Finally, CT2 exhibited mostly downregulated genes upon Fol-pt infection. This included genes involved in transcription regulation, defense responses, and metal ion binding.

CONCLUSIONS

Results suggest that CT1 mounts a defense response against Fol-pt. IAC391 exhibits an intermediate phenotype whereby some defense response genes are activated, and others are suppressed. Finally, the transcriptional profile in the CT2 hints towards lower levels of resistance. Fo-npt also induced transcriptional changes in all cultivars, but to a lesser extent. Results of this study will support genetic breeding programs currently underway in the zone.

Pathogenesis-Related Genes of PR1, PR2, PR4, and PR5 Families Are Involved in the Response to Fusarium Infection in Garlic (Allium sativum L.)

Plants of the genus Allium developed a diversity of defense mechanisms against pathogenic fungi of the genus Fusarium, including transcriptional activation of pathogenesis-related (PR) genes. However, the information on the regulation of PR factors in garlic (Allium sativum L.) is limited. In the present study, we identified AsPR genes putatively encoding PR1, PR2, PR4, and PR5 proteins in A. sativum cv. Ershuizao, which may be involved in the defense against Fusarium infection. The promoters of the AsPR1-5 genes contained jasmonic acid-, salicylic acid-, gibberellin-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with the response to plant parasites. The expression of AsPR1c, d, g, k, AsPR2b, AsPR5a, c (in roots), and AsPR4a(c), b, and AsPR2c (in stems and cloves) significantly differed between garlic cultivars resistant and susceptible to Fusarium rot, suggesting that it could define the PR protein-mediated protection against Fusarium infection in garlic. Our results provide insights into the role of PR factors in A. sativum and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.

Genome-Wide Identification and Expression of Chitinase Class I Genes in Garlic (Allium sativum L.) Cultivars Resistant and Susceptible to Fusarium proliferatum

Vegetables of the Allium genus are prone to infection by Fusarium fungi. Chitinases of the GH19 family are pathogenesis-related proteins inhibiting fungal growth through the hydrolysis of cell wall chitin; however, the information on garlic (Allium sativum L.) chitinases is limited. In the present study, we identified seven class I chitinase genes, AsCHI1–7, in the A. sativum cv. Ershuizao genome, which may have a conserved function in the garlic defense against Fusarium attack. The AsCHI1–7 promoters contained jasmonic acid-, salicylic acid-, gibberellins-, abscisic acid-, auxin-, ethylene-, and stress-responsive elements associated with defense against pathogens. The expression of AsCHI2, AsCHI3, and AsCHI7 genes was constitutive in Fusarium-resistant and -susceptible garlic cultivars and was mostly induced at the early stage of F. proliferatum infection. In roots, AsCHI2 and AsCHI3 mRNA levels were increased in the susceptible and decreased in the resistant cultivar, whereas in cloves, AsCHI7 and AsCHI5 expression was decreased in the susceptible but increased in the resistant plants, suggesting that these genes are involved in the garlic response to Fusarium proliferatum attack. Our results provide insights into the role of chitinases in garlic and may be useful for breeding programs to increase the resistance of Allium crops to Fusarium infections.

Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

BACKGROUND

The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms.

RESULTS

Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution.

CONCLUSIONS

Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa

Mycogone perniciosa causes wet bubble disease in Agaricus bisporus and various Agaricomycetes species. In a previous work, we identified 41 GH18 chitinase genes and other pathogenicity-related genes in the genome of M. perniciosa Hp10. Chitinases are enzymes that degrade chitin, and they have diverse functions in nutrition, morphogenesis, and pathogenesis. However, these important genes in M. perniciosa have not been fully characterized, and their functions remain unclear. Here, we performed a genome-wide analysis of M. perniciosa GH18 genes and analyzed the transcriptome profiles and GH18 expression patterns in M. perniciosa during the time course of infection in A. bisporus. Phylogenetic analysis of the 41 GH18 genes with those of 15 other species showed that the genes were clustered into three groups and eight subgroups based on their conserved domains. The GH18 genes clustered in the same group shared different gene structures but had the same protein motifs. All GH18 genes were localized in different organelles, were unevenly distributed on 11 contigs, and had orthologs in the other 13 species. Twelve duplication events were identified, and these had undergone both positive and purifying selection. The transcriptome analyses revealed that numerous genes, including transporters, cell wall degrading enzymes (CWDEs), cytochrome P450, pathogenicity-related genes, secondary metabolites, and transcription factors, were significantly upregulated at different stages of M. perniciosa Hp10 infection of A. bisporus. Twenty-three out of the 41 GH18 genes were differentially expressed. The expression patterns of the 23 GH18 genes were different and were significantly expressed from 3 days post-inoculation of M. perniciosa Hp10 in A. bisporus. Five differentially expressed GH18 genes were selected for RT-PCR and gene cloning to verify RNA-seq data accuracy. The results showed that those genes were successively expressed in different infection stages, consistent with the previous sequencing results. Our study provides a comprehensive analysis of pathogenicity-related and GH18 chitinase genes’ influence on M. perniciosa mycoparasitism of A. bisporus. Our findings may serve as a basis for further studies of M. perniciosa mycoparasitism, and the results have potential value for improving resistance in A. bisporus and developing efficient disease-management strategies to mitigate wet bubble disease.

Lilium regale Wilson WRKY2 Regulates Chitinase Gene Expression During the Response to the Root Rot Pathogen Fusarium oxysporum

Root rot, mainly caused by Fusarium oxysporum, is the most destructive disease affecting lily (Lilium spp.) production. The WRKY transcription factors (TFs) have important roles during plant immune responses. To clarify the effects of WRKY TFs on plant defense responses to pathogens, a WRKY gene (LrWRKY2) was isolated from Lilium regale Wilson, which is a wild lily species highly resistant to F. oxysporum. The expression of LrWRKY2, which encodes a nuclear protein, is induced by various hormones (methyl jasmonate, ethephon, salicylic acid, and hydrogen peroxide) and by F. oxysporum infection. In this study, LrWRKY2-overexpressing transgenic tobacco plants were more resistant to F. oxysporum than the wild-type plants. Moreover, the expression levels of jasmonic acid biosynthetic pathway-related genes (NtAOC, NtAOS, NtKAT, NtPACX, NtJMT, NtOPR, and NtLOX), pathogenesis-related genes (NtCHI, NtGlu2, and NtPR-1), and antioxidant stress-related superoxide dismutase genes (NtSOD, NtCu-ZnSOD, and MnSOD) were significantly up-regulated in LrWRKY2 transgenic tobacco lines. Additionally, the transient expression of a hairpin RNA targeting LrWRKY2 increased the susceptibility of L. regale scales to F. oxysporum. Furthermore, an F. oxysporum resistance gene (LrCHI2) encoding a chitinase was isolated from L. regale. An electrophoretic mobility shift assay demonstrated that LrWRKY2 can bind to the LrCHI2 promoter containing the W-box element. Yeast one-hybrid assay results suggested that LrWRKY2 can activate LrCHI2 transcription. An examination of transgenic tobacco transformed with LrWRKY2 and the LrCHI2 promoter revealed that LrWRKY2 activates the LrCHI2 promoter. Therefore, in L. regale, LrWRKY2 is an important positive regulator that contributes to plant defense responses to F. oxysporum by modulating LrCHI2 expression.

Salicylate-Induced Chitinases in Pea Roots

Three proteins induced by salicylic acid were revealed in pea roots. These proteins were identified as chitinase isozymes belonging to the glycoside hydrolases family 18. The PsCam050724 transcript encoding at least one of these isoforms was found, allowing us to determine its primary structure, which lacks the signal peptide.