Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales.
ABSTRACT: The order Magnaporthales (Ascomycota, Fungi) includes devastating pathogens of cereals, such as the rice blast fungus Pyricularia (Magnaporthe) oryzae, which is a model in host-pathogen interaction studies. Magnaporthales also includes saprotrophic species associated with grass roots and submerged wood. Despite its scientific and economic importance, the phylogenetic position of Magnaporthales within Sordariomycetes and the interrelationships of its constituent taxa, remain controversial. In this study, we generated novel transcriptome data from 21 taxa that represent key Magnaporthales lineages of different infection and nutrition modes and phenotypes. Phylogenomic analysis of >200 conserved genes allowed the reconstruction of a robust Sordariomycetes tree of life that placed the monophyletic group of Magnaporthales sister to Ophiostomatales. Among Magnaporthales, three major clades were recognized: 1) an early diverging clade A comprised of saprotrophs associated with submerged woods; 2) clade B that includes the rice blast fungus and other pathogens that cause blast diseases of monocot plants. These species infect the above-ground tissues of host plants using the penetration structure, appressorium; and 3) clade C comprised primarily of root-associated species that penetrate the root tissue with hyphopodia. The well-supported phylogenies provide a robust framework for elucidating evolution of pathogenesis, nutrition modes, and phenotypic characters in Magnaporthales.
Project description:The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.
Project description:Ophioceras is accommodated in the monotypic family Ophioceraceae (Magnaporthales, Sordariomycetes), and the genus is delimited based on molecular data. During an ongoing survey of bambusicolous fungi in southwest China, we collected a submerged decaying branch of bamboo from Sichuan Province, China and an Ophioceras species occurring on this substrate was observed and isolated. An Ophioceras taxon was delimited based on morphological characteristics and combined LSU, RPB1 and ITS sequence analyses and is described as Ophioceras sichuanense sp. nov. The species formed a well-supported clade basal to Ophioceras (100% ML, 1.00 PP). Based on the updated phylogenetic tree of Magnaporthales, Ceratosphaerella castillensis (generic type) and C. rhizomorpha formed a clade within Ophioceras and morphologically resemble Ophioceras. Therefore, Ceratosphaerella is synonymized under Ophioceras. The phylogenetic relationships of Ophioceras are discussed in relation to morphological similarities of genera in Magnaporthales. The generic circumscription of Ophioceras is emended.
Project description:The order Magnaporthales belongs to Sordariomycetes, Ascomycota. Magnaporthales includes five families, namely Ceratosphaeriaceae, Pseudohalonectriaceae, Ophioceraceae, Pyriculariaceae, and Magnaporthaceae. Most Magnaporthales members are found in Poaceae plants and other monocotyledonous herbaceous plants ubiquitously as plant pathogens or endophytic fungi, and some members are found in decaying wood or dead grass as saprophytic fungi. Therefore, studying the biogeography and ecology of Magnaporthales is of great significance. Here, we described the biodiversity of endophytic Magnaporthales fungi from Poaceae at three latitudes in China and conducted a meta-analysis of the geography and ecology of Magnaporthales worldwide. We found that Magnaporthales is a dominant order in the endophytic fungi of Poaceae. More than half of the endophytic Magnaporthales fungi have a taxonomically uncertain placement. Notably, few endophytic fungi are grouped in the clusters with known saprophytic or pathogenic Magnaporthales fungi, indicating that they may have saprophytic and parasitic differentiation in nutritional modes and lifestyles. The meta-analysis revealed that most species of Magnaporthales have characteristic geographical, host, and tissue specificity. The geographical distribution of the three most studied genera, namely <i>Gaeumannomyces</i>, <i>Magnaporthiopsis</i>, and <i>Pyricularia</i>, in Magnaporthales may depend on the distribution of their hosts. Therefore, studies on the endophytic fungal Magnaporthales from monocotyledonous plants, including Poaceae, in middle and low latitudes will deepen our understanding of the biogeography and ecology of Magnaporthales.
Project description:The present paper represents the fifth contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data. This paper focuses on 11 genera of microfungi, for seven of which the type species are neo- or epitypified here: Arthrinium (Arthrinium caricicola; Apiosporaceae, Xylariales, Sordariomycetes), Ceratosphaeria (Ceratosphaeria lampadophora; Magnaporthaceae, Magnaporthales, Sordariomycetes), Dimerosporiopsis (Dimerosporiopsis engleriana; Venturiaceae, Venturiales, Dothideomycetes), Hormodochis (Hormodochis melanochlora; Stictidaceae, Ostropales, Ostropomycetidae, OSLEUM clade, Lecanoromycetes), Lecanostictopsis (Lecanostictopsis kamatii; Mycosphaerellaceae, Capnodiales, Dothideomycetes), Lembosina (Lembosina aulographoides; Lembosinaceae fam. nov., Lembosinales ord. nov., Dothideomycetes), Neomelanconium (Neomelanconium gelatosporum; Cenangiaceae, Helotiales, Leotiomycetes), Phragmotrichum (Phragmotrichum chailletii; Melanommataceae, Pleosporales, Pleosporomycetidae, Dothideomycetes), Pseudomelanconium gen. nov. (Pseudomelanconium spartii; incertae sedis, Pezizomycotina), Rutola (Rutola graminis; Torulaceae, Pleosporales, Pleosporomycetidae, Dothideomycetes), and Trullula (Trullula oreoselini; incertae sedis, Pezizomycotina).
Project description:The classification of two root-infecting fungi, Magnaporthe garrettii and M. griffinii, was examined by phylogenetic analysis of multiple gene sequences. This analysis demonstrated that M. garrettii and M. griffinii were sister species that formed a well-supported separate clade in Papulosaceae (Diaporthomycetidae, Sordariomycetes), which clusters outside of the Magnaporthales. Wongia gen. nov, is established to accommodate these two species which are not closely related to other species classified in Magnaporthe nor to other genera, including Nakataea, Magnaporthiopsis and Pyricularia, which all now contain other species once classified in Magnaporthe.
Project description:The present paper represents the second contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data, and where possible, ecology. This paper focuses on 12 genera of microfungi, 11 of which the type species are neo- or epitypified here: Allantophomopsis (A. cytisporea, Phacidiaceae, Phacidiales, Leotiomycetes), Latorua gen. nov. (Latorua caligans, Latoruaceae, Pleosporales, Dothideomycetes), Macrodiplodiopsis (M. desmazieri, Macrodiplodiopsidaceae, Pleosporales, Dothideomycetes), Macrohilum (M. eucalypti, Macrohilaceae, Diaporthales, Sordariomycetes), Milospium (M. graphideorum, incertae sedis, Pezizomycotina), Protostegia (P. eucleae, Mycosphaerellaceae, Capnodiales, Dothideomycetes), Pyricularia (P. grisea, Pyriculariaceae, Magnaporthales, Sordariomycetes), Robillarda (R. sessilis, Robillardaceae, Xylariales, Sordariomycetes), Rutola (R. graminis, incertae sedis, Pleosporales, Dothideomycetes), Septoriella (S. phragmitis, Phaeosphaeriaceae, Pleosporales, Dothideomycetes), Torula (T. herbarum, Torulaceae, Pleosporales, Dothideomycetes) and Wojnowicia (syn. of Septoriella, S. hirta, Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Novel species include Latorua grootfonteinensis, Robillarda africana, R. roystoneae, R. terrae, Torula ficus, T. hollandica, and T. masonii spp. nov., and three new families: Macrodiplodiopsisceae, Macrohilaceae, and Robillardaceae. Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed for the major groups of fungi on the List of Protected Generic Names for Fungi (www.generaoffungi.org).
Project description:Four morphologically similar specimens of an unidentified perithecial ascomycete were collected on decaying wood submerged in fresh water. Phylogenetic analysis of DNA sequences from protein-coding and ribosomal nuclear loci supports the placement of the unidentified fungus together with Achroceratosphaeria in a strongly supported monophyletic clade. The four collections are described as two new species of the new genus Pisorisporium characterised by non-stromatic, black, immersed to superficial perithecial ascomata, persistent paraphyses, unitunicate, persistent asci with an amyloid apical annulus and hyaline, fusiform, cymbiform to cylindrical, transversely multiseptate ascospores with conspicuous guttules. The asexual morph is unknown and no conidia were formed in vitro or on the natural substratum. The clade containing Achroceratosphaeria and Pisorisporium is introduced as the new order Pisorisporiales, family Pisorisporiaceae in the class Sordariomycetes. It represents a new lineage of aquatic fungi. A sister relationship for Pisorisporiales with the Lulworthiales and Koralionastetales is weakly supported by Bayesian inference and maximum likelihood analyses. The systematic position of Pisorisporium among morphologically similar perithecial ascomycetes is discussed.
Project description:Mycoleptodiscus includes plant pathogens, animal opportunists, saprobic and endophytic fungi. The present study presents the first molecular phylogeny and revision of the genus based on four loci, including ITS, LSU, rpb2, and tef1. An extensive collection of Mycoleptodiscus cultures, including ex-type strains from the CBS, IMI, MUCL, BRIP, clinical isolates from the USA, and fresh isolates from Brazil and Spain, was studied morphologically and phylogenetically to resolve their taxonomy. The study showed that Mycoleptodiscus sensu lato is polyphyletic. Phylogenetic analysis places Mycoleptodiscus in Muyocopronales (Dothideomycetes), together with Arxiella, Leptodiscella, Muyocopron, Neocochlearomyces, and Paramycoleptodiscus. Mycoleptodiscus terrestris, the type species, and M. sphaericus are reduced to synonyms, and one new species is introduced, M. suttonii. Mycoleptodiscus atromaculans, M. coloratus, M. freycinetiae, M. geniculatus, M. indicus, M. lateralis (including M. unilateralis and M. variabilis as its synonyms) and M. taiwanensis belong to Muyocopron (Muyocopronales, Dothideomycetes), and M. affinis, and M. lunatus to Omnidemptus (Magnaporthales, Sordariomycetes). Based on phylogenetic analyses we propose Muyocopron alcornii sp. nov., a fungus associated with leaf spots on Epidendrum sp. (Orchidaceae) in Australia, Muyocopron zamiae sp. nov. associated with leaf spots on Zamia (Zamiaceae) in the USA, and Omnidemptus graminis sp. nov. isolated from a grass (Poaceae) in Spain. Furthermore, Neomycoleptodiscus venezuelense gen. & sp. nov. is introduced for a genus similar to Mycoleptodiscus in Muyocopronaceae.
Project description:The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming protein and to discover other amyloid-forming proteins, we searched for all homologs of the HET-s protein in a database of protein domains and fungal genomes, using a combined application of HMM, psi-blast and pGenThreader techniques, and performed a comparative evolutionary analysis of the N-terminal alpha-helical domain and the C-terminal prion-forming domain of HET-s. By assessing the tandem evolution of both domains, we observed that the prion-forming domain is restricted to Sordariomycetes, with a marginal additional sequence homolog in Arthroderma otae as a likely case of horizontal transfer. This suggests innovation and rapid evolution of the solenoid fold in the Sordariomycetes clade. In contrast, the N-terminal domain evolves at a slower rate (in Sordariomycetes) and spans many diverse clades of fungi. We performed a full three-dimensional protein threading analysis on all identified HET-s homologs against the HET-s solenoid fold, and present detailed structural annotations for identified structural homologs to the prion-forming domain. An analysis of the physicochemical characteristics in our set of structural models indicates that the HET-s solenoid shape can be readily adopted in these homologs, but that they are all less optimized for fibril formation than the P. anserina HET-s sequence itself, due chiefly to the presence of fewer asparagine ladders and salt bridges. Our combined structural and evolutionary analysis suggests that the HET-s shape has "limited scope" for amyloidosis across the wider protein universe, compared to the 'generic' left-handed beta helix. We discuss the implications of our findings on future identification of amyloid-forming proteins sharing the solenoid fold.