Amir Sharon

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

Early Events in the Fusarium verticillioides-Maize Interaction Characterized by Using a Green Fluorescent Protein-Expressing Transgenic Isolate

ABSTRACT The infection of maize by Fusarium verticillioides can result in highly variable disease symptoms ranging from asymptomatic plants to severe rotting and wilting. We produced F. verticillioides green fluorescent protein-expressing transgenic isolates and used them to characterize early events in the F. verticillioides-maize interaction that may affect later symptom appearance. Plants grown in F. verticillioides-infested soil were smaller and chlorotic. The fungus colonized all of the underground parts of a plant but was found primarily in lateral roots and mesocotyl tissue. In some mesocotyl cells, conidia were produced within 14 to 21 days after infection. Intercellular mycelium was detected, but additional cells were not infected until 21 days after planting. At 25 to 30 days after planting, the mesocotyl and main roots were heavily infected, and rotting developed in these tissues. Other tissues, including the adventitious roots and the stem, appeared to be healthy and contained only a small number of hyphae. These results imply that asymptomatic systemic infection is characterized by a mode of fungal development that includes infection of certain tissues, intercellular growth of a limited number of fungal hyphae, and reproduction of the fungus in a few cells without invasion of other cells. Development of visibly rotted tissue is associated with massive production of fungal mycelium and much less organized growth.

Fungal apoptosis: function, genes and gene function

Cells of all living organisms are programmed to self-destruct under certain conditions. The most well known form of programmed cell death is apoptosis, which is essential for proper development in higher eukaryotes. In fungi, apoptotic-like cell death occurs naturally during aging and reproduction, and can be induced by environmental stresses and exposure to toxic metabolites. The core apoptotic machinery in fungi is similar to that in mammals, but the apoptotic network is less complex and of more ancient origin. Only some of the mammalian apoptosis-regulating proteins have fungal homologs, and the number of protein families is drastically reduced. Expression in fungi of animal proteins that do not have fungal homologs often affects apoptosis, suggesting functional conservation of these components despite the absence of protein-sequence similarity. Functional analysis of Saccharomyces cerevisiae apoptotic genes, and more recently of those in some filamentous species, has revealed partial conservation, along with substantial differences in function and mode of action between fungal and human proteins. It has been suggested that apoptotic proteins might be suitable targets for novel antifungal treatments. However, implementation of this approach requires a better understanding of fungal apoptotic networks and identification of the key proteins regulating apoptotic-like cell death in fungi.

Use of green fluorescent protein (GFP) for studying development and fungal-plant interaction in Cochliobolus heterostrophus

The green fluorescent protein (GFP) has been widely used as an extremely useful vital marker in a large number of organisms, but good expression in filamentous ascomycetes has not been reported. To facilitate the research of fungal development and fungal-plant interaction, we constructed two plasmid vectors for the expression of the synthetic SGFP-TYG gene in ascomycete species, and used these vectors for transformation of the maize pathogen Cochliobolus heterostrophus. High level expression of GFP was obtained, as detected by anti-GFP antibodies and by fluorescence microscopy. The intense fluorescence was used as a highly efficient vital marker to detect cytoplasmic and developmental changes that occur in the fungus, and to follow phytopathogenic development of the fungus on and inside maize leaves. The hyphae within the leaf form a unique parallel growth pattern, closely associated with, and apparently determined by, the anatomy of the leaf. Fluorescence intensity was quantified by digital analysis of the green fluorescence image and was highly correlated with the amount of mycelium and levels of disease. Expression of GFP was obtained in additional ascomycetes that were transformed with the new constructs, indicating that SGFP-TYG can be used as a highly effective vital marker in ascomycetes.

Pathogenic and Nonpathogenic Lifestyles in Colletotrichum acutatum from Strawberry and Other Plants

ABSTRACT Anthracnose is one of the major fungal diseases of strawberry occurring worldwide. In Israel, the disease is caused primarily by the species Colletotrichum acutatum. The pathogen causes black spot on fruit, root necrosis, and crown rot resulting in mortality of transplants in the field. The host range and specificity of C. acutatum from strawberry was examined on pepper, eggplant, tomato, bean, and strawberry under greenhouse conditions. The fungus was recovered from all plant species over a 3-month period but caused disease symptoms only on strawberry. Epiphytic and endophytic (colonization) fungal growth in the different plant species was confirmed by reisolation from leaf tissues and by polymerase chain reaction (PCR)-specific primer amplification. C. acutatum was also isolated from healthy looking, asymptomatic plants of the weed genera Vicia and Conyza. Isolates that were recovered from the weeds caused disease symptoms on strawberry and were positively identified as C. acutatum by PCR. The habitation of a large number of plant species, including weeds, by C. acutatum suggests that, although it causes disease only on strawberry and anemone in Israel, this fungus can persist on many other plant species. Therefore, plants that are not considered hosts of C. acutatum may serve as a potential inoculum source for strawberry infection and permit survival of the pathogen between seasons.

Anti-Apoptotic Machinery Protects the Necrotrophic Fungus Botrytis cinerea from Host-Induced Apoptotic-Like Cell Death during Plant Infection

Necrotrophic fungi are unable to occupy living plant cells. How such pathogens survive first contact with living host tissue and initiate infection is therefore unclear. Here, we show that the necrotrophic grey mold fungus Botrytis cinerea undergoes massive apoptotic-like programmed cell death (PCD) following germination on the host plant. Manipulation of an anti-apoptotic gene BcBIR1 modified fungal response to PCD-inducing conditions. As a consequence, strains with reduced sensitivity to PCD were hyper virulent, while strains in which PCD was over-stimulated showed reduced pathogenicity. Similarly, reduced levels of PCD in the fungus were recorded following infection of Arabidopsis mutants that show enhanced susceptibility to B. cinerea. When considered together, these results suggest that Botrytis PCD machinery is targeted by plant defense molecules, and that the fungal anti-apoptotic machinery is essential for overcoming this host-induced PCD and hence, for establishment of infection. As such, fungal PCD machinery represents a novel target for fungicides and antifungal drugs.

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Genomics and domestication of wheat Modern wheat, which underlies the diet of many across the globe, has a long history of selection and crosses among different species. Avni et al. used the Hi-C method of genome confirmation capture to assemble and annotate the wild allotetraploid wheat (Triticum turgidum). They then identified the putative causal mutations in genes controlling shattering (a key domestication trait among cereal crops). They also performed an exome capture–based analysis of domestication among wild and domesticated genotypes of emmer wheat. The findings present a compelling overview of the emmer wheat genome and its usefulness in an agricultural context for understanding traits in modern bread wheat. Science, this issue p. 93 A polyploid wheat genome assembly elucidates wheat domestication history. Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat’s domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.

In Planta Production of Indole-3-Acetic Acid by Colletotrichum gloeosporioides f. sp. aeschynomene

ABSTRACT The plant pathogenic fungus Colletotrichum gloeosporioides f. sp. aeschynomene utilizes external tryptophan to produce indole-3-acetic acid (IAA) through the intermediate indole-3-acetamide (IAM). We studied the effects of tryptophan, IAA, and IAM on IAA biosynthesis in fungal axenic cultures and on in planta IAA production by the fungus. IAA biosynthesis was strictly dependent on external tryptophan and was enhanced by tryptophan and IAM. The fungus produced IAM and IAA in planta during the biotrophic and necrotrophic phases of infection. The amounts of IAA produced per fungal biomass were highest during the biotrophic phase. IAA production by this plant pathogen might be important during early stages of plant colonization.

Transformation of the bioherbicide Colletotrichum gloeosporioides f. sp. Aeschynomene By electroporation of germinated conidia.

Abstract A highly efficient and reproducible procedure for the transformation of the bioherbicide Colletotrichum gloeosporioides f. sp. aeschynomene by electroporation of germinated conidia is reported. Development of the procedure involved a detailed study of the germination process followed by extensive calibration of the electrical-pulse and selection conditions. Optimization of the transformation protocol was facilitated by the use of the green fluorescent protein that helped in the identification of stable transformants and in a fast assessment of transgene expression levels, colony homogeneity and genetic stability. Under optimal conditions, over 80 stable transformants/cuvette were obtained. Plasmid integration was predominantly homologous, but high transformation rates were obtained both with homologous and non-homologous vectors. The method described not only opens up opportunities for the genetic manipulation of C. gloeosporioides f. sp. aeschynomene, but also provides a framework for the development and optimization of transformation in other fungi.

Ethylene sensing and gene activation in Botrytis cinerea: a missing link in ethylene regulation of fungus-plant interactions?

Ethylene production by infected plants is an early resistance response leading to activation of plant defense pathways. However, plant pathogens also are capable of producing ethylene, and ethylene might have an effect not only on the plant but on the pathogen as well. Therefore, ethylene may play a dual role in fungus-plant interactions by affecting the plant as well as the pathogen. To address this question, we studied the effects of ethylene on the gray mold fungus Botrytis cinerea and the disease it causes on Nicotiana benthamiana plants. Exposure of B. cinerea to ethylene inhibited mycelium growth in vitro and caused transcriptional changes in a large number of fungal genes. A screen of fungal signaling mutants revealed a Galpha null mutant (deltabcg1) which was ethylene insensitive, overproduced ethylene in vitro, and showed considerable transcriptional changes in response to ethylene compared with the wild type. Aminoethoxyvinylglycine (AVG)-treated, ethylene-nonproducing N. benthamiana plants developed much larger necroses than ethylene-producing plants, whereas addition of ethylene to AVG-treated leaves restricted disease spreading. Ethylene also affected fungal gene expression in planta. Expression of a putative pathogenicity fungal gene, bcspl1, was enhanced 24 h after inoculation in ethylene-producing plants but only 48 h after inoculation in ethylene-nonproducing plants. Our results show that the responses of B. cinerea to ethylene are partly mediated by a G protein signaling pathway, and that ethylene-induced plant resistance might involve effects of plant ethylene on both the plant and the fungus.