Smut fungi (Basidiomycota p.p., Ascomycota p.p.) of the world. novelties, selected examples, trends

Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis

Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.

How Do Smut Fungi Use Plant Signals to Spatiotemporally Orientate on and In Planta?

Smut fungi represent a large group of biotrophic plant pathogens that cause extensive yield loss and are also model organisms for studying plant-pathogen interactions. In recent years, they have become biotechnological tools. After initial penetration of the plant epidermis, smut fungi grow intra-and intercellularly without disrupting the plant-plasma membrane. Following the colonialization step, teliospores are formed and later released. While some smuts only invade the tissues around the initial penetration site, others colonize in multiple plant organs resulting in spore formation distal from the original infection site. The intimate contact zone between fungal hyphae and the host is termed the biotrophic interaction zone and enables exchange of signals and nutrient uptake. Obviously, all steps of on and in planta growth require fine sensing of host conditions as well as reprogramming of the host by the smut fungus. In this review, we highlight selected examples of smut fungal colonization styles, directional growth in planta, induction of spore formation, and the signals required, pointing to excellent reviews for details, to draw attention to some of the open questions in this important research field.

Resurgence of Less-Studied Smut Fungi as Models of Phytopathogenesis in the Omics Age

The smut fungi form a large, diverse, and nonmonophyletic group of plant pathogens that have long served as both important pests of human agriculture and, also, as fertile organisms of scientific investigation. As modern techniques of molecular genetic analysis became available, many previously studied species that proved refractive to these techniques fell by the wayside and were neglected. Now, as the advent of rapid and affordable next-generation sequencing provides genomic and transcriptomic resources for even these "forgotten" fungi, several species are making a comeback and retaking prominent places in phytopathogenic research. In this review, we highlight several of these smut fungi, with special emphasis on Microbotryum lychnidis-dioicae, an anther smut whose molecular genetic tools have finally begun to catch up with its historical importance in classical genetics and now provide mechanistic insights for ecological studies, evolution of host-pathogen interaction, and investigations of emerging infectious disease.

Cryptic diversity in the Antherospora vaillantii complex on Muscari species

The anther smut fungi in the ustilaginomycetous genus Antherospora (Floromycetaceae, Urocystidales) that infect monocots, are currently placed in nine species. Against the background of the generally observed high host specificity in smut fungi, the broad host range reported for some of the species suggests much higher diversity. Antherospora vaillantii s. lato includes anther smuts on different Muscari species. In this study, specimens of anther smuts on Muscari armeniacum, M. botryoides, M. comosum, and M. tenuiflorum were analysed by rDNA sequences and morphology to determine whether they represented one polyphagous or several host specific species. The molecular phylogeny revealed three distinct lineages that were correlated with host plants, yet had only slight morphological differences. These lineages are assigned to three cryptic species: Antherospora hortensis sp. nov. on Muscari armeniacum, A. muscari-botryoidis comb. nov. (syn. Ustilago muscari-botryoidis) on M. botryoides, and A. vaillantii s. str. on M. comosum and M. tenuiflorum. All species on Muscari form a monophyletic group within Antherospora, and the phylogenetic relations within this group coincide well with the subgeneric classification of the respective host species. This indicates a common ancestry of Muscari anther smuts and co-evolution as a driver of their diversification.

Shivasia gen. nov. for the Australasian smut Ustilago solida that historically shifted through five different genera

The generic position of the enigmatic smut fungus Ustilago solida is evaluated applying molecular phylogenetic analyses using ITS and LSU rDNA sequences as well as light and scanning electron microscopical investigations of several collections of this species. Ustilago solida has previously been included in five different genera (Ustilago, Urocystis, Sorosporium, Cintractia, and Tolyposporium), however, molecular analyses revealed that this smut does not belong to any of these genera and represents a distinct ustilaginalean lineage. The closest known phylogenetic relative of Ustilago solida is Heterotolyposporium lepidospermatis, the type species of the monotypic genus Heterotolyposporium. Both smuts differ considerably in both LSU sequences and in several morphological traits, such as the structure of sori and the characteristics of spore balls. Accordingly, the new genus Shivasia is described to accommodate Ustilago solida. This smut infects different Schoenus species (Cyperaceae) in Australia and New Zealand. The description of Shivasia increases the number of endemic smut genera in Australasia to ten. Compared to all other continents the number of endemic smut genera is exceptionally high, which may point at fast evolving characters and/or may be caused by the regional history, including the long-term geographic isolation of Australasia.