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Despite the interest on fungi as eukaryotic model systems, the molecular mechanisms regulating the fungal non-self-recognition at a distance have not been studied so far. This paper investigates the molecular mechanisms regulating the cross-talk at a distance between two filamentous fungi, Trichoderma gamsii and Fusarium graminearum which establish a mycoparasitic interaction where T. gamsii and F. graminearum play the roles of mycoparasite and prey, respectively. In the present work, we use an integrated approach involving dual culture tests, comparative genomics and transcriptomics to investigate the fungal interaction before contact (‘sensing phase’). Dual culture tests demonstrate that growth rate of F. graminearum accelerates in presence of T. gamsii at the sensing phase. T. gamsii up-regulates the expression of a ferric reductase involved in iron acquisition, while F. graminearum up-regulates the expression of genes coding for transmembrane transporters and killer toxins. At the same time, T. gamsii decreases the level of extracellular interaction by down-regulating genes coding for hydrolytic enzymes acting on fungal cell wall (chitinases). Given the importance of fungi as eukaryotic model systems and the ever-increasing genomic resources available, the integrated approach hereby presented can be applied to other interactions to deepen the knowledge on fungal communication at a distance.

Fusarium graminearum is among the main causal agents of Fusarium head blight (FHB), or scab, of wheat and other cereals, caused by a complex of Fusarium species, worldwide. Besides causing economic losses in terms of crop yield and quality, F. graminearum poses a severe threat to animal and human health. Here, we present the first draft whole-genome sequence of the mycotoxigenic Fusarium graminearum strain ITEM 124, also providing useful information for comparative genomics studies.

Background Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi. Results We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc. Conclusions This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2917-6) contains supplementary material, which is available to authorized users.

Trichoderma gamsii T6085 is a promising beneficial isolate whose effects consist of growth inhibition of the main agents causing Fusarium head blight, reduction of mycotoxin accumulation, competition for wheat debris, and reduction of the disease in both the lab and the field. Here, we present the first genome assembly of a T. gamsii isolate, providing a useful platform for the scientific community.

Fusarium graminearum is among the main causal agents of Fusarium head blight (FHB), or scab, of wheat and other cereals, caused by a complex of Fusarium species, worldwide. Besides causing economic losses in terms of crop yield and quality, F. graminearum poses a severe threat to animal and human health. Here, we present the first draft whole-genome sequence of the mycotoxigenic Fusarium graminearum strain ITEM 124, also providing useful information for comparative genomics studies.

Trichoderma harzianum T6776 is a promising beneficial isolate whose effects consist of growth promotion, positive response of photosynthetic activity, hormonal signaling, and carbon partitioning in tomato, coupled with biocontrol of plant pathogens. Here, we present the first genome assembly of T6776, providing a useful platform for the scientific community.

In 2012, Colletotrichum isolates were collected from field-grown safflower (Carthamus tinctorius) crops in central Italy from plants exhibiting typical anthracnose symptoms. Colletotrichum isolates were also collected from seed surfaces and from within seeds. The genetic variability of these isolates was assessed by a multilocus sequencing approach and compared with those from Colletotrichum chrysanthemi and Colletotrichum carthami isolates from different geographic areas and other Colletotrichumacutatum sensu lato-related isolates. Phylogenetic analysis revealed that all of the strains isolated from C.tinctorius belonged to the species described as C.chrysanthemi, whereas all of the strains belonging to C.carthami had been isolated from Calendula officinalis. Phenotypic characterization of isolates was performed by assessing growth rates at different temperatures, morphology of colonies on potato dextrose agar (PDA) and the size of conidia. All C.chrysanthemi isolates from safflower had similar growth rates at different temperatures, comparable colony morphologies when grown on PDA and conidial sizes consistent with previously described C.chrysanthemi isolates. Pathogenicity tests were performed by artificially inoculating both seeds and plants and confirmed the seedborne nature of this pathogen. When inoculated on plants, C.chrysanthemi caused the typical symptoms of anthracnose on leaves. This is the first record of this pathogen on C.tinctorius in Italy, and it presents an updated characterization of Colletotrichum isolates pathogenic to safflowers in Europe.

In October 2016, rotting grape berries were detected on grapevine (Vitis vinifera) in Livorno (Nugola, Tuscany, Italy). Symptoms on grape berry skins varied from circular brown spots to rotting fruits. Both berries and petioles were covered with creamy salmon-colored masses of conidia. Rotten grape berries lost turgor and turned into ‘mummies’ over time. Symptoms suggested that a member of the genus Colletotrichum could be involved. Single spore cultures were obtained from conidial masses and grown in the laboratory at 25°C with a 12-h light period on potato dextrose agar (PDA). Monoconidial isolates had light gray cottony aerial mycelium with colony color ranging from whitish to dark gray, while the reverse ranged from whitish to salmon-pink. Conidia were hyaline and unicellular, cylindrical or clavate, and often with a light median constriction. However, Colletotrichum spp. are often difficult to distinguish morphologically. Total genomic DNA was extracted from monoconidial isolate SS354. The ITS region of rDNA and partial GAPDH, CHS-1, HIS3, ACT, and TUB2 genes were amplified and sequenced according to Damm et al. (2012). Sequences were deposited in GenBank (accession no. KY293406 for ITS, KY293407 for TUB, KY293403 for CHS, KY293405 for HIS3, KY293402 for ACT, and KY293404 for GAPDH). The multilocus phylogenetic analysis carried out with the obtained and reference sequences (Damm et al. 2012) revealed that the SS354 isolate clustered within C. godetiae. Pathogenicity tests were performed in laboratory by inoculating detached grape berries with or without petioles at the petiole insertion point with 20 µl of a conidial suspension (105 conidia/ml) of the isolate SS354. Grape berries without petiole developed symptoms similar to those observed in the field. Fungal colonies reisolated from the lesions on berries were morphologically identical to isolate SS354. Control grape berries inoculated with sterile water remained healthy as well as grape berries with petioles inoculated with the pathogen. This suggests that C. godetiae is able to infect wounded grape berries. However, information regarding other infection routes were not searched, as this was not the aim of this work. This is the first report of C. godetiae causing grape berry rot in Italy. The phylogenetic analysis reveals that C. godetiae SS354 is closely related to C. godetiae RB118, the causal agent of anthracnose on grapevine in the U.K. (Baroncelli et al. 2014). Since C. godetiae is polyphagous, cross-infections between grape and other crops are possible. Remarkably, Cacciola et al. (2012) reported C. clavatum (syn. C. godetiae) as the prevalent Colletotrichum species associated with epidemic outbreaks of olive anthracnose in Italy. However, at present, no information regarding cross-infection of C. godetiae between grapevine and olive are available. Due to the high economic and social value of wine production in Italy (in 2013 only in Tuscany the production of grapes accounted for 8 million tons), a monitoring plan based on simple molecular identification tools should be advisable.

Phylogenetic analysis of the 133 Colletotrichum spp. listed in Additional file 1: Table S1 based on a multilocus concatenated alignment of the ITS, TUB2, ACT and GAPDH genes. A Markov Chain Monte Carlo (MCMC) algorithm was used to generate phylogenetic trees with Bayesian probabilities using MrBayes 3.2.1. The species complexes described by Cannon et al. [2] and Liu et al. [49] as well as C. acutatum species complex clades described by Damm et al. [5] are shown. Monilochaetes infuscans was used as an outgroup. (PDF 593 kb)

International audience; Clonostachys rosea is a mycoparasitic fungus that can control several important plant diseases. Here, we report on the genome sequencing of C. rosea and a comparative genome analysis, in order to resolve the phylogenetic placement of C. rosea and to study the evolution of mycoparasitism as a fungal lifestyle. The genome of C. rosea is estimated to 58.3 Mb, and contains 14,268 predicted genes. A phylogenomic analysis shows that C. rosea clusters as sister taxon to plant pathogenic Fusarium species, with mycoparasitic/ saprotrophic Trichoderma species in an ancestral position. A comparative analysis of gene family evolution reveals several distinct differences between the included mycoparasites. Clonostachys rosea contains significantly more ATP-binding cassette (ABC) transporters , polyketide synthases, cytochrome P450 monooxygenases, pectin lyases, glucose-methanol-choline oxidoreductases, and lytic polysaccharide monooxygenases compared with other fungi in the Hypocreales. Interestingly, the increase of ABC transporter gene number in C. rosea is associated with phylogenetic subgroups B (multidrug resistance proteins) and G (pleiotropic drug resistance transporters), whereas an increase in subgroup C (multidrug resistance-associated proteins) is evident in Trichoderma virens. In contrast with mycoparasitic Trichoderma species, C. rosea contains very few chitinases. Expression of six group B and group G ABC transporter genes was induced in C. rosea during exposure to the Fusarium mycotoxin zearalenone, the fungicide Boscalid or metabolites from the biocontrol bacterium Pseudomonas chlororaphis. The data suggest that tolerance toward secondary metab-olites is a prominent feature in the biology of C. rosea.