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Cryopreservation has the potential for long-term germplasm storage. The metabolic pathways and gene regulation involved in cryopreservation procedures are still not well documented. Hence, the genetic expression profile was evaluated using RNA-Seq in zygotic embryos of grapevines subjected to cryopreservation by vitrification. Sequencing was performed on the Illumina NextSeq 500. The average alignment of reads was 96% against the reference genome. The expression profiles showed 229 genes differentially expressed (186 repressed and 46 induced). The main biological processes showing upregulated enrichment were related to nucleosome assembly, while downregulated processes were related to organ growth. The most highly repressed processes were associated with the organization of the cell wall and membrane components. The unnamed protein product and 17.3 kDa class II heat shock protein (HSP) were highly induced, while ATPase subunit 1 and expansin-A1 were repressed. The response to the cooling and warming process during cryopreservation probably indicates that the changes occurring in transcription may be related to epigenetics. In addition, the cell exhibits an increase in the reserve of nutrients while seeking to survive modestly using available energy and pausing the plant's development. Additionally, energy containment occurred to cope with the stress caused by the treatment where deactivation of components of the cell membrane was observed, possibly due to changes in fluidity caused by alterations in temperature.

Fruit losses and wastage are mainly due to postharvest diseases; their control is reduced with pesticides. The excessive use of synthetic fungicides has caused harmful effects on human health and the environment, so it is therefore necessary to reduce their use. The development of new innocuous strategies has led to the use of compounds of natural or biological origin with the capacity to induce the plant defense system, which improves the fruit’s response against future pathogen attacks in addition to reducing the incidence of postharvest diseases. These compounds are known as “elicitors”. Although the use of molecular tools such as RT-qPCR or the measurement of the enzymatic activity of molecular markers makes it possible to determine the activation of the plant defense system in response to the application of an elicitor compound, in recent years, omics technologies such as the transcriptome, proteome, or metabolome have provided new and interesting information that helps to elucidate the molecular aspects involved in the activation of the plant defense system in response to the application of elicitors. This review summarizes recent advances in molecular aspects, highlighting the contribution of omics technologies to a better understanding of fruit defense mechanisms induced by different elicitors.

Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, either indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma spp. emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to cocultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell wall–degrading enzymes putatively relevant for root colonization. Repression of such genes reached their basal levels at later times in the interaction, when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell wall–degrading enzymes with the auxiliary activities class. RNA-Seq analyses showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (increased protection of Arabidopsis-1). Sequence analyses of IPA-1 showed its closest relatives to be members of the Rad5/Rad16 and SNF2 subfamilies; however, it grouped into a different clade. Although deletion of IPA-1 in T. virens did not affect its growth, the antibiotic activity of Δipa-1 culture filtrates against Rhizoctonia solani diminished but it remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared with the wild type.

The accumulation of cold temperature is an important factor for the release of bud dormancy in grapevine. The stress generated by cold is related to changes in defense hormones such as salicylic acid (SA). To understand the participation of this hormone during grapevine bud dormancy release, in this study, we evaluated the effects of cold accumulation on the endogenous SA content and expression patterns of the synthesis and signaling genes of SA as well as budbreak rates. Buds were subjected to an accumulation of 900 or 600 chilling units (CUs). The budbreak percentage was determined when cold-treated buds were transferred to warm temperatures (25 °C). The percentage of budbreak was closely correlated with the amount of cumulative CUs; the percentage increased gradually with the amount of chilling applied before forcing. The increase in the expression level of the SA biosynthesis gene (ICS2) and the endogenous SA content were quantified in cold-treated buds, and the expression was correlated with the percentage of budbreak. These findings may indicate that in dormant grapevine buds, cold accumulation stimulates the synthesis of SA. In cold-treated buds, the cellular levels of SA led to the expression of the NPR1 and PR1 genes, which was mediated by the transcription factor WRKY70. In contrast, expression of NPR1 and PR1 in control buds, which maintained a basal level of SA, and expression of ICS2 and WRKY70 were not detected, suggesting that the constitutive expression of NPR1-SA is independent. Taken together, the results of this study suggest a possible involvement of the SA signaling pathway in grapevine bud dormancy release.

Objetivo: caracterizar la cadena productiva de guanábana en el municipio de Compostela, Nayarit, México, y describir las áreas de oportunidad y sus riesgos para proponer un orden de intervención de esa cadena productiva que establezca los puntos críticos de control que deben implementarse para impulsar la comercialización de guanábana mexicana en el mercado internacional. Metodología: partiendo de fuentes de información directas e indirectas, se construyó una base metodológica que consta de cinco fases diseñadas para calcular el OI óptimo. Resultados: La Cadena Productiva de Guanábana de Compostela se compone de tres eslabones primarios: producción, procesamiento y comercialización, compuestos por actores que cumplen labores específicas. Se identificaron puntos débiles de alto riesgo, así como los Puntos de Control Críticos en la Cadena Productiva de la Guanábana. En base al análisis de relevancia de cada Punto Crítico de Control se construyó un Orden de Intervención diseñado para configurar a la Cadena Productiva de la Guanábana como una opción de desarrollo regional exitosa. Limitaciones: La información disponible del sistema productivo y poscosecha de la guanábana es relativamente escaza. Generar este tipo de información representa un área de oportunidad que requiere el acercamiento con los actores que conforman la cadena. Conclusiones: La presencia de guanábana de Compostela en mercados internacionales de alto valor se ve limitada por riesgos presentes en su cadena productiva. La naturaleza perecedera del fruto destaca como el riesgo principal, y se agrava por riesgos fitosanitarios, mala coordinación entre eslabones, técnicas de manejo desactualizadas e infraestructura de almacenamiento y transporte deficiente. Se estima que implementar el Orden de Intervención incrementaría las ganancias de la Cadena Productiva de la Guanábana al menos 175% en un corto a mediano plazo.

La vid es un cultivo importante en México y Sonora es líder en producción. Sin embargo, no existe un método adecuado para la conservación del germoplasma. La crioconservación (almacenamiento en nitrógeno líquido (NL)) es una alternativa para la conservación a largo plazo e involucra técnicas de crioprotección (vitrificación y encapsulación-deshidratación) para evitar el daño celular durante el congelamiento. En este trabajo se evaluó la pérdida iónica de yemas de vid sometidas a crioconservación mediante vitrificación y encapsulación deshidratación. Para la vitrificación las yemas fueron sometidas a PVS2 por 0-180 min. En la encapsulacióndeshidratación, las yemas encapsuladas se deshidrataron y se cuantificó la humedad. Finalmente se almacenaron en NL por tres segundos, una hora, un día, una semana y un mes. Se observó que a los 60 min con PVS2 la pérdida iónica fue similar al control. La humedad de las yemas encapsuladas alcanzó un 23 % a las 8 h. La pérdida iónica en las yemas crioconservadas mediante vitrificación varió entre 6-23 % y en la encapsulación-deshidratación del 7-30 %. La crioconservación mediante vitrificación y encapsulación-deshidratación protegió a las yemas en los tiempos en NL, sin embargo en la vitrificación el daño fue menor

The aim of the present study was to investigate the inhibitory mechanisms of quercetin against L. monocytogenes biofilm formation, by affecting secretion of polymeric substances (EPS) and spatio-temporal organization. The minimum concentration of quercetin inhibiting the establishment of bacterial biofilm was determined to be 0.8 mM; therefore, a lower concentration of the flavonoid (0.2 mM) was used in order to investigate its effect on cell attachment and EPS production on stainless steel and the spatio-temporal organization on glass, while avoiding bias of loss of cellular viability. In applying this concentration, reductions of 1.32 and 1.94 Log10 CFU/cm2 of initial adhesion and maximum cell density on stainless steel were observed on the test surfaces at 2 h (initial adhesion) and 24 h (maximum cell density), respectively. EPS on mature biofilms (24 h) was mainly composed by proteins (97.83%), followed by polysaccharides (2.03%) and DNA (0.14%). In addition, quercetin reduced total extracellular protein content by 41% compared with control; while, DNA and polysaccharide contents in biofilms were not affected. Also, relative to control, quercetin impaired surface colonization, early stages of biofilm formation and the development of a more complex architecture during its formation. This proved that quercetin inhibited the formation of L. monocytogenes biofilms by reducing initial attachment, the amount of extracellular proteins found in the EPS matrix and the overall spatio-temporal organization of L. monocytogenes.

Mucormycosis is a life-threatening fungal infection caused by various ubiquitous filamentous fungi of the Mucorales order, although Rhizopus spp. and Mucor spp. are the most prevalent causal agents. The limited therapeutic options available together with a rapid progression of the infection and a difficult early diagnosis produce high mortality. Here, we developed an adult zebrafish model of Mucor circinelloides infection which allowed us to confirm the link between sporangiospore size and virulence. Transcriptomic studies revealed a local, strong inflammatory response of the host elicited after sporangiospore germination and mycelial tissue invasion, while avirulent and UV-killed sporangiospores failed to induce inflammation and were rapidly cleared. Of the 857 genes modulated by the infection, those encoding cytokines, complement factors, peptidoglycan recognition proteins, and iron acquisition are particularly interesting. Furthermore, neutrophils and macrophages were similarly recruited independently of sporangiospore virulence and viability, which results in a robust depletion of both cell types in the hematopoietic compartment. Strikingly, our model also reveals for the first time the ability of mucormycosis to induce the apoptosis of recruited macrophages but not neutrophils. The induction of macrophage apoptosis, therefore, might represent a key virulence mechanism of these fungal pathogens, providing novel targets for therapeutic intervention in this lethal infection.

Tomato cultivation generates great profits for Mexico; however, the distribution of the fruit faces limitations due to the postharvest losses caused by its rapid deterioration. The reduction in fruit firmness is due in part to the degradation of pectin located in the primary cell wall. Several fruits such as strawberry (Fragaria × ananassa), tomato (Solanum lycopersicum L.) and mango (Mangifera indica L.) show an increase in the expression of genes that code for the enzyme rhamnogalacturonan lyase (RGL) during ripening. In tomato RGL is encoded by a family of 13 multigenes, of which three are active in the fruit. Rhamnogalacturonan l (RG-l) is a polysaccharide that is part of the pectins of the cell wall and is degraded by the RGL enzyme. Thus, the study of changes of RGL in the expression of genes that code for RGL during the development and ripening of tomato fruit will help to elucidate the physiological function of this family of genes. The objective of the present study was to assess the expression profile of genes Solyc04g076630, Solyc04g076660 and Solyc11g011300 and the ethylene production during the development and ripening of the tomato fruit. The Solyc11g011300 gene showed an increase in activity that correlated with the increase in ethylene production in fruits, suggesting that this gene plays a role in the loss of firmness of the fruit during ripening. The high levels of expression of genes Solyc04g076630 and Solyc04g076660 recorded during fruit development suggest their participation in the re-engineering of the RG-I polymer during the initial stages of fruit development.

La crioconservacion ha revolucionado el campo de la biotecnologia. Congelar en nitrogeno liquido (NL) preserva celulas por largo tiempo. En ese sentido, en este trabajo se evaluaron tres condiciones de crioconservacion basados en la vitrificacion de yemas de vid. Las yemas fueron sometidas a PVS2, PVS3 y glicerol por 0-420 min, y colocadas en NL por una hora. De modo posterior a cada tiempo de incubacion se cuantifico la perdida de iones como medida de viabilidad y se evaluo el dano mediante observacion en estereoscopio. Basados en el porcentaje de viabilidad el mejor metodo fue empleando PVS3 (30% viabilidad), seguido de glicerol (25%) y PVS2 (

Regulation of genes involved in nitrogen metabolism likely plays a role in the ability of fungi to exploit and survive under different environmental situations. To learn about the mechanism of adaptation of the biotrophic fungus Ustilago maydis from a medium containing a source of fixed nitrogen, to a medium depending on the ability to fix N2 by its bacterial endosymbiont, we explored gene expression profiles using RNA-Seq analyses under these two conditions. The differentially expressed (DE) fungal genes were analyzed, identifying 90 genes that were regulated 24 h after shifting the fungus to media lacking ammonium nitrate as a nitrogen source. From these, mRNA levels were increased for 49 genes, whereas 41 were down-regulated. The functional description associated to the regulated genes revealed that nine key pathways were represented, including, secondary metabolism, the metabolism of nitrogen, amino acid, fatty acid, amino sugar and nucleotide sugar, purine, peroxisome, and the regulation of actin cytoskeleton. These results suggest that the interplay of U. maydis with its N2 fixing bacterial endosymbiont is a flexible process that may be active during the adaptation of the fungus to the different nitrogen sources.

In this chapter, knowledge on the development of plant biology and technology to obtain food from horticultural products from when humans started to domesticate and improve different plant species until the development of genome edition techniques is described. In this context, an overview is given of the first efficient protocol for DNA sequencing, the development of plant genetic engineering, and the creation of the first transgenic plants, including a perspective about genetically modified organisms. The creation of the next-generation sequencing protocols to generate massive data on DNA sequencing, computers, and bioinformatics tools gave rise to the “omics” era. These tools, along with the new genome edition technologies, make it possible to obtain a better understanding of plant biology and give the scientific capacity to design horticultural products with almost any desirable organoleptic, nutritional, or postharvest shelf-life.

Quantitative transcriptome analysis led to the identification of 331 transcripts regulated by white light. Evaluation of the response to white light in mutants affected in the previously characterized blue-light receptor Blr1, demonstrated the existence of both Blr1-dependent and independent responses. Functional categorization of the light responsive genes indicated the effect of light on regulation of various transcription factors, regulators of chromatin structure, signaling pathways, genes related to different kinds of stress, metabolism, redox adjustment, and cell cycle among others. In order to establish the participation of other photoreceptors, gene expression was validated in response to different wavelengths. Gene regulation by blue and red light suggests the involvement of several photoreceptors in integrating light signals of different wavelengths in Trichoderma atroviride. Functional analysis of potential blue light photoreceptors suggests that several perception systems for different wavelengths are involved in the response to light. Deletion of cry1, one of the potential photoreceptors, resulted in severe reduction in the photoreactivation capacity of the fungus, as well as a change in gene expression under blue and red light.

The available genomic and proteomic information of non-model organisms is often underrepresented in public databases hindering their study at molecular, cellular, and physiological levels. Information on Zabrotes subfasciatus (Mexican bean weevil) is poorly represented in databases, yet it is a major pest of common beans. We report the transcriptome of Z. subfasciatus larvae; transcripts were sequenced using an Illumina RNA-Seq technology and assembled de novo identifying 29,029 unigenes with an average size of 1168 bp and an N50 value of 2196 bp. About 15,124 unigenes (52%) were functionally annotated and categorized. Further analysis revealed 30 unigene sequences encoding putative targets of the insecticidal PF2 lectin. The complete deduced amino acid sequences of eight selected proteins potentially related to insecticidal mechanism of Palo Fierro 2 (PF2) were used for predicting probable N-glycosylation sites and analyzing phylogenetic relationships with insect sequences. This work provides a dramatic increase in the genetic resources available for Coleopterans and set the basis for developing future studies on biological aspects and potential control strategies for Z. subfasciatus.

Marine bivalve hatchery productivity is continuously challenged by apparition and propagation of new diseases, mainly those related to vibriosis. Disinfectants and antibiotics are frequently overused to prevent pathogen presence, generating a potential negative impact on the environment. Recently, the use of highly diluted compounds with immunostimulant properties in marine organisms has been trailed successfully to activate the self-protection mechanisms of marine bivalves. Despite their potential as immunostimulants, little is known about their way of action. To understand their effect, a comparative transcriptomic analysis was performed with Argopecten ventricosus juveniles. The experimental design consisted of four treatments formulated from pathogenic Vibrio lysates at two dilutions: [(T1) Vibrio parahaemolyticus and Vibrio alginolyticus 1D; (T2) V. parahaemolyticus and V. alginolyticus 7C]; minerals [(T3) PhA+SiT 7C], scorpion venom [(T4) ViT 31C]; and one control (C1) hydro-alcoholic solution (ethanol 1%). The RNA sequencing (RNAseq) analysis showed a higher modulation of differentially expressed genes (DEG) in mantle tissue compared to gill tissue. The scallops that showed a higher number of DEG related to immune response in mantle tissue corresponded to T1 (V. parahaemolyticus and V. alginolyticus lysate) and T3 (Silicea terra® - Phosphoric acid®). The transcriptome analysis allowed understanding some interactions between A. ventricosus juveniles and highly-diluted treatments.

The present study explored the effect of quercetin on the expression of virulence genes actA, inlA, inlC, and their regulatory components, sigB and prfA, in L. monocytogenes. Furthermore, the physicochemical changes on the surface, membrane permeability, and biofilm formation of quercetin-treated bacteria were evaluated. An inhibitory dose-dependent effect of quercetin (0.1–0.8 mM) was observed on the cell attachment on stainless steel at 2 and 6 h at 37 °C. Quercetin at 0.8 mM prevented the biofilm formation on stainless steel surfaces after 6 h of incubation at 37 °C, while the untreated bacteria formed biofilms with a cell density of 5.1 Log CFU/cm2. The microscopic analysis evidenced that quercetin at 0.2 mM decreased the biovolume and covered area of the attached micro-colonies. Also, sigB, prfA, inlA, inlC, and actA genes were downregulated by 7–29 times lower compared to untreated bacteria. In addition, quercetin decreased the superficial cell charge, increased the membrane permeability, and its surface hydrophobicity. These results demonstrated that quercetin prevented biofilm formation, repressed the genes of stress and virulence of L. monocytogenes and also altered the physicochemical cell properties.

Background: Red oak pollen is an important cause of allergic respiratory disease and it is widely distributed in North America and central Europe. To date, however, red oak pollen allergens have not been identified. Here, we describe the allergenic protein profile from red oak pollen. Methods: Total proteins were extracted from red oak pollen using a modified phenolic extraction method, and, subsequently, proteins were separated by two-dimensional gel electrophoresis (2DE) for both total protein stain (Coomassie Blue) and immunoblotting. A pool of 8 sera from red oak sensitive patients was used to analyze blotted proteins. Protein spots were analyzed by Mass Spectrometry. Results: Electrophoretic pattern of total soluble proteins showed higher intensity bands in the regions of 26–40 and 47–52 kDa. Two dimensional immunoblots using pool sera from patients revealed four allergenic proteins spots with molecular masses in the range from 50 to 55 kDa. Mass spectrometry analysis identified 8 proteins including Enolase 1 and Enolase 1 chloroplastic, Xylose isomerase (X1 isoform), mitochondrial Aldehyde dehydrogenase, UTP-Glusose-1-phosphate uridylyltransferase, Betaxylosidase/alpha-l-arabinofuranosidase and alpha- and beta subunits of ATP synthase. Conclusions: This study has identified for first time 8 IgE binding proteins from red oak pollen. These findings will pave the way towards the development of new diagnostic and therapeutic modalities for red oak allergy. Keywords: Immunoproteomics, Mass spectrometry, Pollen allergy, Red oak, Two-dimensional gel electrophoresis

All organisms are constantly exposed to adverse environmental conditions including mechanical damage, which may alter various physiological aspects of growth, development and reproduction. In plant and animal systems, the damage response mechanism has been widely studied. Both systems posses a conserved and sophisticated mechanism that in general is aimed at repairing and preventing future damage, and causes dramatic changes in their transcriptomes, proteomes, and metabolomes. These damage-induced changes are mediated by elaborate signaling networks, which include receptors/sensors, calcium (Ca(2+)) influx, ATP release, kinase cascades, reactive oxygen species (ROS), and oxylipin signaling pathways. In contrast, our current knowledge of how fungi respond to injury is limited, even though various reports indicate that mechanical damage triggers reproductive processes. In fungi, the damage response mechanism has been studied more in depth in Trichoderma atroviride. Interestingly, these studies indicate that the mechanical damage response involves ROS, Ca(2+), kinase cascades, and lipid signaling pathways. Here we compare the response to mechanical damage in plants, animals and fungi and provide evidence that they appear to share signaling molecules and pathways, suggesting evolutionary conservation across the three kingdoms.

Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq. Approximately 400 million reads were generated and de novo assembled into 107,744 unigenes, with a mean length of 1,717 bp and with this information an online Mango RNA-Seq Database (http://bioinfo.bti.cornell.edu/cgi-bin/mango/index.cgi) which is a valuable genomic resource for molecular research into the biology of mango fruit was created. RNA-Seq analysis suggested that the pathway leading to biosynthesis of the cuticle component, cutin, is up-regulated during overripening. This data was supported by analysis of the expression of several putative cuticle-associated genes and by gravimetric and microscopic studies of cuticle deposition, revealing a complex continuous pattern of cuticle deposition during fruit development and involving substantial accumulation during ripening/overripening.

Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. Results: We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. Conclusions: The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop., La lista completa de autores que integran el documento puede consultarse en el archivo., Facultad de Ciencias Exactas, Instituto de Biotecnologia y Biologia Molecular

SUMMARY The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei , T. atroviride , and T. virens , and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N -linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N -linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma , and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

A conserved injury-defense mechanism is present in plants and animals, in which the production of reactive oxygen species (ROS) and lipid metabolism are essential to the response. Here, we describe that in the filamentous fungus Trichoderma atroviride , injury results in the formation of asexual reproduction structures restricted to regenerating cells. High-throughput RNA-seq analyses of the response to injury in T. atroviride suggested an oxidative response and activation of calcium-signaling pathways, as well as the participation of lipid metabolism, in this phenomenon. Gene-replacement experiments demonstrated that injury triggers NADPH oxidase (Nox)–dependent ROS production and that Nox1 and NoxR are essential for asexual development in response to damage. We further provide evidence of H 2 O 2 and oxylipin production that, as in plants and animals, may act as signal molecules in response to injury in fungi, suggesting that the three kingdoms share a conserved defense-response mechanism.

Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Results Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. Conclusions The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.