ABSTRACT Fusarium virguliforme causes the Sudden Death Syndrome, an important disease in soybean crops. In this work, we investigated the defensive response mechanisms in soybean root, at cell wall level, during F. virguliforme infection using an in vitro culture system. We measured total root lignin content by the acetyl bromide method and estimated the in-situ lignin and suberin deposition by confocal microscopy on local and systemic root tissues, i.e. adjacent and distant to the pathogen entry site respectively. Moreover, the expression dynamics of phenylalanine ammonia lyase (PAL), shikimate/quinate hydroxycinnamoyltransferase (HCT) and cinnamyl alcohol dehydrogenase (CAD) was evaluated by real-time quantitative PCR. The results showed that, although the most significant increment of lignin deposition was observed in the epidermal cells of local tissues, F. virguliforme also induced lignin deposition changes in a sistemic fashion. In fact, inoculated plants presented a higher deposition of lignin in hypodermis and cortex than the control ones, independently of the distance from the inoculum source, while suberin deposition was higher in local zones. Moreover, the gene expression analysis showed an up-regulation of PAL, HCT and CAD genes after the inoculation with the pathogen, which correlates with the cell wall modifications observed in the local tissues. The results presented here suggest that the increase in lignin and suberin deposition during soybean root/ F. virguliforme interaction is probably a strategy not only to stop the pathogen entrance, but to provide the plant more time to prepare its defences as well.

Abstract Capsicum includes ca. 41 species of chili peppers. In this original report we PCR amplified, cloned, sequenced and characterized the 5S rDNA non-transcribed spacer -NTS- in 23 taxa of nine clades of Capsicum, divergent at geographical origin and fruit and chromosome traits, and compared the NTS features throughout Solanaceae. According to GC content, inner variability and regulatory elements, the NTS organizes into three distinct structural regions; genetic variability at the NTS in Capsicum and related genus clusters into defined taxa hierarchies. Based on the reconstruction of a maximum-likelihood phylogenetic tree and phylogenetic networks, NTS sequences of Capsicum and related taxa grouped into well recognized categories -genus, section, clade, species, variety-. An evolutionary scenario arose from combined genetic and phylogenetic NTS data, in which monophyly and lineage diversification over time of Capsicum are addressed. Our analysis is original to include all domesticated species of Capsicum prevailing in germplasm collections and breeding programs, together with a large group of wild taxa that demanded further genetic characterization. The NTS set up as a double purpose marker in Capsicum, to directly evaluate genetic variability and reconstruct phylogenetic relationships to a broad extent, and constitutes a valuable tool for germplasm characterization and evolutionary studies within Solanaceae.

Macrophomina phaseolina is a generalist soil-borne fungus present all over the world. It cause diseases such as stem and root rot, charcoal rot and seedling blight. Under high temperatures and low soil moisture, this fungus can cause substantial yield losses in crops such as soybean, sorghum and groundnut. The wide host range and high persistence of M. phaseolina in soil as microsclerotia make disease control challenging. Therefore, understanding the basis of the pathogenicity mechanisms as well as its interactions with host plants is crucial for controlling the pathogen. In this work, we aim to describe the general characteristics and pathogenicity mechanisms of M. phaseolina, as well as the hosts defense response. We also review the current methods and most promising forecoming ones to reach a responsible control of the pathogen, with minimal impacts to the environment and natural resources.

The soil-borne pathogen Setophoma terrestris is the causal agent of pink root of onion, one of the most challenging diseases in onion production. Conventional approaches for managing the disease like solarization, soil fumigation and crop rotation have not been proven effective enough. In this work, we evaluated the biocontrol capacity of Bacillus subtilis ALBA01 (BsA01) against S. terrestris, in a highly susceptible onion cultivar, both under greenhouse and field conditions. Disease incidence and severity were evaluated together with growth, photosynthesis among other physiological variables, and yield parameters. When compared with plants infected with the pathogen, those plants co-inoculated with BsA01 showed significantly less damage and levels of biocontrol above 50%. With regard to physiological parameters, plants challenged with S. terrestris and inoculated with BsA01 performed as well as the control non-infected plants revealing a growth promotion effect of BsA01 on onion plants.

Soil-borne pathogen Setophoma terrestris is the causal agent of pink root of onion, one of the most challenging diseases in onion production. Conventional approaches for managing the disease like solarization, soil fumigation and crop rotation have not been proven effective enough. In this work, we evaluated the biocontrol capacity of Bacillus subtilis ALBA01 (BsA01) against S. terrestris , in a highly susceptible onion cultivar, both under greenhouse and field conditions. Disease incidence and severity were evaluated together with growth, photosynthesis among other physiological variables and yield parameters. When compared with plants infected with the pathogen, those plants co-inoculated with BsA01 showed significantly less damage and levels of biocontrol above 50%. With regard to physiological parameters, plants challenged with S terrestris and inoculated with BsA01 performed as well as the control non-infected plants revealing a growth promotion effect of BsA01 on onion plants.

The soil-borne fungal plant pathogen Verticillium dahliae can infect more than 300 plant species including important economic crops, causing great economic loses. V. dahliae can persist and survive more than 14 years in the soil by resistance structures, known as microsclerotia, which constitute the primary inoculum in the field. In vitro mass production of microsclerotia is essential for performing many pathological assays. Nevertheless to harvest the microsclerotia is not an easy task and several protocols have been described although none of them is completely satisfying for different reasons. here we present a new protocol that is reproducible, robust, simple and fast allows to overcome the difficulties for obtaining massive amounts of microsclerotia. In summary, we developed a new culture medium that we called Pluronic Potato Medium (PPM) because it is essentially potato dextrose media with the hydrogel, Pluronic F127 as a solidifying agent. The microsclerotia collected in form PPM were infectious in tomato plants were they were able to reproduce the disease and we recovered and quantitated V. dahliae in infected plants.

The life-cycle of Puccinia sorghi, a heteroecious fungus, consists of five well-defined spore stages. The uredinial and telial stages are completed on the primary host (maize) whereas spermagonial and aecial stages occur on Oxalis spp., a perennial and widespread weed. Portions of corn leaves with telia were surface sterilized and placed in Petri dishes with 2% water agar and maintained in a growth chamber at 25 ± 1 °C and photoperiod of 16 h light and 8 h dark for 48 h to induce the formation of basidia and basidiospores. Oxalis conorrhiza plants were inoculated with those basidiospores, to confirm the generation of spermagonia with spermatia, and subsequently aecia with aeciospores. Corn plants were then inoculated with aeciospores to confirm the formation of urediospores and teliospores. The aecial phase of common corn rust was confirmed to occur on O. conhorriza and the descriptions of spore stages in Argentina are now reported in this work, confirming a potential sexual source of variability of P. sorghi. The natural occurrence of aecial infections on O. conhorriza in Córdoba may play an important role in generating new variants of P. sorghi in Argentina, allowing a constant adaptation of the pathogen to the environment of the different corn production zones.

Capsicum comprises 35 species of chili peppers and five of them are cultivated worldwide as spices or vegetables. Diploid karyotypes based in x = 12 and x = 13 are common in Capsicum and the constitutive heterochromatin (cHet) is of particular interest in the genus since it is largely variable, particularly its highly GC-rich fraction. However, the repetitive DNA components of this heterochromatic regions are unknown. Given the co-localization of rDNA loci with the CMA (+) DAPI-heterochromatic bands, we tested the hypothesis that the highly GC rich cHet fraction is composed of the whole 18S-25S ribosomal DNA (rDNA) unit or some of its components. Here we report on a novel satellite for Capsicum and Solanaceae composed of the complete rDNA unit. We physically mapped six Capsicum derived specific 18S-25S rDNA probes that covered the entire span of the rDNA unit and analysed a DraI restriction product on eight chromosomally different taxa of Capsicum, representative of the major phylogenetic clades of chili peppers. The co-localization of every gene and spacer probes of the 18S-25S rDNA unit suggest their structural function as a major repetitive component of the highly GC-rich cHet in Capsicum species with x = 12. In addition, analyses of the clones derived from restriction assays in C. pubescens suggested that the differential functional status of 18S-25S rDNA loci (nucleolar organizer regions-NOR5-or cHet) in this species is related to a divergence in a short sequence upstream the regulatory transcription initiation site (TIS) of the intergenic spacer (IGS). The results here provided evidence that an rDNA mega satellite played a significant role in the evolution of the karyotype features of x = 12 Capsicwn species. The finding of a mega satellite family derived from the whole rDNA unit is a novelty for plant genomes.

Soilborne pathogens represent a threat to agriculture causing important yield losses. The “Sudden Death Syndrome” (SDS), a severe disease in soybean is caused by a complex of Fusarium species. This pathosystem has been widely investigated and several strategies were proposed to manage SDS. Although a decrease in symptoms and in the level of root tissue infection particularly by F. virguliforme was observed in presence of arbuscular mycorrhizal fungi (AMF), biological control based on AMF has received less attention. Here we report the results, under strict in vitro culture experimental conditions, a transcriptional analysis in mycorrhizal versus non-mycorrhizal soybean plantlets upon infection by F. virguliforme. An important transcriptional reprogramming was detected following infection by the pathogen. Results revealed 1768 and 967 differentially expressed genes in the AMF-colonized (+AMF+Fv) and non-colonized (−AMF+Fv) plants, respectively. Major transcriptional changes, corresponded to defence response related genes belonging to secondary metabolism, stress and signalling categories. The +AMF+Fv treatment showed the largest number of upregulated genes related to defence, as those encoding for disease resistance proteins, WRKY transcription factors, auxins, receptors kinases, and proteases. Only few genes had primed expression in +AMF+Fv treatment, as those coding for a thaumatin-like protein (TLP) and a pleiotropic drug resistance (PDR) protein. Moreover, +AMF+Fv showed a significant number of downregulated genes related to cell wall modification and peroxidases than – AMF+Fv treatment. This detailed insight increases our knowledge on the transcriptional changes and the potential metabolic pathways involved in the enhanced resistance/tolerance of mycorrhizal plants upon infection with F. virguliforme.

Macrophomina phaseolina is a soil-borne fungal pathogen with a wide host range that causes charcoal rot in soybean [Glycine max (L.) Merr.]. Control of the disease is a challenge, due to the absence of genetic resistance and effective chemical control. Alternative or complementary measures are needed, such as the use of biological control agents, in an integrated approach. Several studies have demonstrated the role of arbuscular mycorrhizal fungi (AMF) in enhancing plant resistance or tolerance to biotic stresses, decreasing the symptoms and pressure caused by various pests and diseases, including M. phaseolina in soybean. However, the specific contribution of AMF in the regulation of the plant response to M. phaseolina remains unclear. Therefore, the objective of the present study was to investigate, under strict in-vitro culture conditions, the global transcriptional changes in roots of premycorrhized soybean plantlets challenged by M. phaseolina (+AMF+Mp) as compared with nonmycorrhizal soybean plantlets (-AMF+Mp). MapMan software was used to distinguish transcriptional changes, with special emphasis on those related to plant defense responses. Soybean genes identified as strongly upregulated during infection by the pathogen included pathogenesis-related proteins, disease-resistance proteins, transcription factors, and secondary metabolism-related genes, as well as those encoding for signaling hormones. Remarkably, the +AMF+Mp treatment displayed a lower number of upregulated genes as compared with the -AMF+Mp treatment. AMF seemed to counteract or balance costs upon M. phaseolina infection, which could be associated to a negative impact on biomass and seed production. These detailed insights in soybean-AMF interaction help us to understand the complex underlying mechanisms involved in AMF-mediated biocontrol and support the importance of preserving and stimulating the existing plant-AMF associates, via adequate agricultural practices, to optimize their agro-ecological potential.

In this work, we described an in vitro system adequate for investigating the pathosystem soybean/arbuscular mycorrhizal fungi (AMF)/Fusarium virguliforme. Pre-mycorrhized plantlets with Rhizophagus irregularis were infected by F. virguliforme either locally via a plug of gel supporting mycelium (Method 1) or via a macroconidia suspension applied to the medium surface (Method 2). Root colonization by the AMF and infection by the pathogen were similar to the usual observations in pot experiments. Within a period of 18 days, more than 20% of the roots were colonized by the AMF and infection by the pathogen was observed in all the plants. In presence of AMF, a decrease in symptoms and in the level of root tissue infection was noticed. With Method 1, smaller necrotic lesions were observed in the pre-mycorrhized plantlets. In Method 2, pathogen infection was slower but more homogenous. These results demonstrated the suitability of the in vitro cultivation system to study the pathosystem soybean/AMF/F. virguliforme. We propose this in vitro cultivation system for studying the mechanisms involved in the biocontrol conferred by AMF against F. virguliforme in soybean.

El ciclo de vida de Puccinia sorghi Schw., organismo causal de la roya comun del maiz, implica como hospedante principal al maiz, como alternativo especies de Oxalis y la generacion de cinco estadios de esporas. En el mundo se hayan reportes de Ps. sobre diez especies de Oxalis (Biswanath, Das; 2016).En Argentina infecciones de Ps. se encontraron en ambientes naturales sobre O. corniculata en Pergamino, provincia de Buenos Aires (Godoy, 1932) y sobre O. conorrhiza en la provincia de Cordoba (Guerra et. al, 2016) aunque hasta el momento no se habia registrado la produccion de basidiosporas infectivas. Estas infecciones son catalogadas como poco habituales y limitadas a algunas regiones templadas del mundo, excluyendo a America del Sur (White, 1999).

ABSTRACT Bacillus subtilis is a nonpathogenic bacterium that lives in soil and has long been used as biological control agent in agriculture. Here, we report the genome sequence of a B. subtilis strain isolated from rhizosphere of onion that shows strong biological activity against the soilborne fungal pathogen Setophoma terrestris.

Despite the importance of mycorrhizal symbiosis, we understand little how different soil managements affect arbuscular mycorrhizal fungi (AMF) communities. Crop rotation is recommended in sustainable agriculture because of its benefits in soil fertility improvement and positive effect decreasing soil borne diseases incidence and pest abundance. Amplicon sequencing of LSU and SSU rRNA gene fragments was used to analyse AMF diversity in fields from one of the most productive regions in Argentina, which varied in the main class of the plant component included in the crop rotation scheme. The samples encompassed different agricultural settings; one involving only monocot plants in the crop rotation schemes, one including a dicot crop, and the other an alternation and/or a combination of monocot and dicot plant components. We found lower richness and diversity in soils under monocot succession than in a dicot/monocot rotation or consociation. We observed that agricultural management had an influence on beta diversity patterns. Principal coordinate analysis showed that communities from the dicot/monocot rotation or consociation samples clustered together and separated from the monocots samples. These findings suggested that the increment of soil AMF diversity is more dependent on the alternation between monocot and dicot crops than other factors related to the farming systems. (C) 2015 Elsevier B.V. All rights reserved.

HomePlant DiseaseVol. 100, No. 2First Report of Oxalis conorrhiza as Alternate Host of Puccinia sorghi, Causal Agent of Common Rust of Maize PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Oxalis conorrhiza as Alternate Host of Puccinia sorghi, Causal Agent of Common Rust of MaizeF. A. Guerra, E. Brücher, R. L. De Rossi, M. C. Plazas, G. D. Guerra, and D. A. DucasseF. A. GuerraSearch for more papers by this author, E. BrücherSearch for more papers by this author, R. L. De RossiSearch for more papers by this author, M. C. PlazasSearch for more papers by this author, G. D. GuerraSearch for more papers by this author, and D. A. DucasseSearch for more papers by this authorAffiliationsAuthors and Affiliations F. A. Guerra , Universidad Católica de Córdoba-Unidad Asociada a Conicet, CP:X5016DHK, Córdoba, Argentina E. Brücher R. L. De Rossi M. C. Plazas G. D. Guerra , Facultad de Ciencias Agropecuarias, Universidad Católica de Córdoba, Argentina D. A. Ducasse , Facultad de Ciencias Agropecuarias, Universidad Católica de Córdoba, and IPAVE-CIAP Instituto Nacional de Tecnología Agropecuaria (INTA), Argentina. Published Online:19 Dec 2015https://doi.org/10.1094/PDIS-05-15-0506-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat A high genetic variability has been recognized in Puccinia sorghi in Argentina (Gonzalez et al. 2011), although its origin remains unclear since the different reported alternate hosts (Oxalis corniculata L., O. stricta L., O. bowiei Herb. ex Lindl.) have never been detected with this disease in the region. In the spring of 2013 and 2014, the spermagonium and aecial estages of a Puccina sp., were observed on O. conorrhiza Jacq. (syn. O. cordobensis R. Knuth) in Córdoba Province, in central Argentina. Those structures were found in 22 sampling sites, under natural infections, in a radius of 175 km of Córdoba City. O. conorrhiza is a bulbous perennial plant native to South America in the Oxalidaceae family, with a low, moderate growth habit. It is distributed in several provinces of central Argentina. O. conorrhiza can usually be found in alluvial flatlands, riverbanks, wasteland, roadsides, pastures, as well as farmlands. The confirmation of the O. conorrhiza species was carried out by the ACCOR Herbarium of the National University of Córdoba, Argentina. On approximately one-third of the leaves of each infected plant, ampulliform, subepidermal, amphigenous spermagonia, arranged in small clusters of 0.5 mm were observed. Spermagonia containing spermatia and receptive hyphae were golden yellow to orange yellow with abundant nectar exuding. Those in the center of the lesion are surrounded by annular groups of aecia, formed exclusively on the abaxial surface of the leaves. Aecia were orange, cylindrical short, with irregular opening at the apex. To determine the causal organism, aesciospores were inoculated in sweet corn plants. Fifty aeciospores from disease samples were suspended per ml of sterile water and sprayed on 5 sweet corn plants. As a negative control, 5 plants were inoculated with sterile water. All plants were kept in the dark at saturated humidity for 24 h at 24°C. After that, the plants were kept at 25 to 27°C and 70 to 80% humidity with a photoperiod of 16 h light. Seven days after inoculation, typical symptoms of corn common rust were observed: orange uredia with abundant urediospores production. At 21 days, typical teleutospores were observed. The rust matched the morphological characteristics of P. sorghi Schwein (Lindquist 1982). DNA from aeciospores from O. conorrhiza was extracted with NucleoSpin Plant II kit. A fragment from the 28S subunit regions rRNA gene was amplified and sequenced with primers Rust1 and F36 (Kropp et al. 1995). BLAST analysis of 28S sequence data (GenBank Accession Nos. HQ412650.1, GU057994.1, and AY114291.1) showed 99% identity to P. sorghi. To our knowledge, this is the first report of P. sorghi isolated from O. conorrhiza worldwide. The report contributes to an improved understanding of variability of P. sorghi which will be useful for exploring appropriate disease management, epidemiology, and breeding strategies.References:Gonzalez, M. del P., et al. 2011. Trop. Plant Pathol. 36:195. ISI, Google ScholarKropp, B. R., et al. 1995. Weed Sci. 43:467. Crossref, ISI, Google ScholarLindquist, J. C. 1982. Colección Científica Vol. 20. Royas de la República Argentina y Zonas Limítrofes, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina. Google ScholarDetailsFiguresLiterature CitedRelated Vol. 100, No. 2 February 2016SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 15 Feb 2016Published: 19 Dec 2015First Look: 18 Aug 2015Accepted: 10 Jul 2015 Page: 519 Information© 2016 The American Phytopathological SocietyCited byPuccinia sorghi (common rust of maize)CABI Compendium, Vol. CABI CompendiumFirst report of the southern corn rust pathogen Puccinia polysora on Zea mays in North Dakota12 October 2021 | Canadian Journal of Plant Pathology, Vol. 43, No. sup2Colletotrichum gloeosporioides causing leaf anthracnose on Oxalis corniculata in Brazil21 November 2019 | Australasian Plant Disease Notes, Vol. 14, No. 1Occurrence of the complete cycle of Puccinia sorghi Schw. in Argentina and implications on the common corn rust epidemiology5 December 2018 | European Journal of Plant Pathology, Vol. 154, No. 2

Pink Root is among the major diseases of onion and its causal agent, Setophoma terrestris , is one of the most severe pathogens in soils of tropical and subtropical climates. The management of Pink Root is difficult and the strategies currently used are ineffective. Although, there are some varieties resistant to S. terrestris , they are not resistant to every isolate of the pathogen and it is not unusual to find isolates that break that resistance. Moreover, chemical control is not technically or economically feasible. So, we decided to address biocontrol as a mean to manage the main onion disease in Argentina. We tested the efficiency of a strain of Bacillus subtilis subsp. subtilis isolated from the rhizosphere of onion plants to inhibit the growth of S. terrestris in vitro . Our strain of Bacillus subtilis showed a strong capacity of growth inhibition of S. terrestris . No antagonistic activity against two other onion pathogens, Fusarium oxysporum f. sp. cepae and F. proliferatum , was observed. Interestingly, we found a high growth inhibition of S. terrestris on plates containing cell-free supernatant of B. subtilis previously grown in the presence of the fungus. No significant differences in the fungal growth were obtained between control plates and plates containing cell-free supernatant from B. subtilis grown without previous contact with S. terrestris . Electron microscopy of S. terrestris from co-cultures plates revealed thickened, tortuous or coiled fungal hyphae, with granules and globular like terminations. These results suggested that the strain of B. subtilis under study has a strong biocontrol activity against S. terrestris and that it would be acting diffusible bacterial inhibitory compounds specifically induced by this pathogen.

Tospoviruses are devastating plant viruses causing severe economic losses in a diverse range of crops worldwide. Here, we describe the development and evaluation of an RNA interference (RNAi) broad-spectrum virus resistance strategy based on a unique and short hairpin-RNA-generating construct (pNhpRNA). This construct was designed from a region of the nucleocapsid gene (N) of Tomato spotted wilt virus (TSWV) that showed a high sequence identity to the corresponding region in the related species Groundnut ringspot virus (GRSV) and Tomato chlorotic spot virus (TCSV). To test the effectiveness of the pNhpRNA construct, we developed a silencing reporter assay based on three fusion proteins in which the complete viral N gene sequence from each of the three tospoviruses was fused in frame to the green fluorescent protein (GFP) sequence. Co-agroinoculation of these constructs with pNhpRNA into leaves of Nicotiana benthamiana resulted in a strong silencing phenotype determined by GFP decay and suppression of the three N genes at the RNA and protein levels. To test the potential of the pNhpRNA construct to generate virus-resistant plants, we infiltrated the whole shoots of N. benthamiana with pNhpRNA. When these infiltrated plants were mechanically inoculated with the mentioned viruses 100, 70, and 60 % resistance phenotypes to TSWV, GRSV, and TCSV, respectively, were observed. The induction of a broad tospovirus resistance with a simple construct and a minimized off-target effect are the main contributions of pNhpRNA.

MicroRNAs (miRNAs) are small ∼20–24 nt species of non-coding RNAs that modulate plant gene expression by means of gene silencing through sequence-specific inhibition of target mRNAs. MiRNAs derive from pol-II transcription of non-coding genes that are precisely processed in nuclear Dicing bodies by a microprocessor complex (dicer-like1–serrate–hyponastic leaves 1: DCL1-SE-HYL1), which recognizes stem-loop secondary-structure features of primary precursor miRNA transcripts (pri-miRNA). The proper processing of the pri-miRNAs results in a double-stranded small RNA that will eventually exit the nucleus and be loaded predominantly onto the effector complex Argonaute1 (Ago1). The single-stranded mature miRNA will guide AGO1, leading to cleavage or translational arrest of complementary mRNAs. MiRNA steady-state levels and activity are regulated not only by transcription rate of precursor transcripts, but also by direct degradation mediated by small RNA degrading nuclease1 (SDN1). miRNAs are retailored by 3′ editing through 2-O-methylation, uridylation and adenlylation, involving Hua enhancer1 (HEN1), HEN1 suppressor1 (HESO1) and probably the exosome—a phenomenon that has been elucidated only scarcely to date in Arabidopsis. MiRNA activity is involved not only in plant development, but also in signaling, abiotic stresses such as drought, heat and metal toxicity, pathogen interaction and symbiotic relationship regulation, among others. The engineering of miRNAs is paving the way to next-generation plant biotechnology by means of over-expression of natural miRNAs, generation of artificial microRNAs and inhibition of miRNA activity by target mimicry. This review highlights the importance of miRNAs in plant sciences by describing the latest updates in this research field.

Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.