Abstract

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.

Abstract

How does a species' ecology affect it's evolutionary trajectory? We seek to answer this question by studying the evolutionary trends of the diverse model Ascomycete genus, Neurospora. Within Neurospora there have been at least nine separate transitions from sexual outbreeding to clonal selfing. Additionally, there has been a transition from a soil and/or dung habitat to a plant and fire associated habitat. Concomitant with this habitat shift has been the evolution of asexual spores. Finally, we describe a new species of conidiating Neurospora that appears to have reverted back to a soil/dung habitat. We analyzed a collection of 181 Neurospora genome sequences from across North America, including populations that vary based on sexual mode, asexual sporulation, and habitat. We found that the transition from sexual outbreeding to clonal selfing leads to a drastic increase in the rate of genomic rearrangements, while the transition to a plant-based habitat (and concomitant evolution of asexual spores) led to reduced diversity within populations. Interestingly, a transition from sexuality to asexuality has not been found within the plant-associated clade. Our study illustrates the profound effects transitions in reproductive systems and habitat can have on the pace and potential for evolution. Furthermore, combined with existing knowledge, we begin to construct a mechanistic model for the four-way interaction between sex, habitat, genome architecture, and population structure.

Abstract

Numerous plant-pathogenic fungi secrete necrotrophic effectors, also known as host-selective toxins, that are important determinants of pathogenicity and virulence. Corynespora cassiicola is a destructive fungal pathogen causing emerging target spot epidemics on crops in the southeastern U.S. Populations of C. cassiicola from cotton, soybean, and tomato have recently been determined to be host specialized. We hypothesize that variation in necrotrophic effectors underlies specificity. The necrotrophic effector cassiicolin was previously identified as a toxin and virulence factor of C. cassiicola causing Corynespora Leaf Fall of rubber tree. Among isolates of C. cassiicola, cassiicolin was encoded by 6 cas gene variants, named cas1 through cas6. To identify variation among putative necrotrophic effector genes in C. cassiicola causing outbreaks in the southeastern U.S. we conducted comparative genomic analyses of 12 C. cassiicola genomes, with 4 each from cotton, soybean and tomato from different regions of the southeastern U.S. The genomes were compared with the reference genome of C. cassiicola (Corca1) from rubber tree. The genomes were assembled de novo and searched for known cas, Tox, and other homologs of effector-encoding genes. Putative secondary metabolite synthetic clusters were identified using antiSMASH. Three cas variants were identified among the 12 genomes; however, no cas genes were identified among the genomes of the tomato isolates. Of the four genomes from soybean isolates, 2 contained only cas6, one contained only cas2, and one contained both cas2 and cas6 variants. The genomes of the four isolates from cotton all contained both cas2 and a new, previously undescribed variant we named cas7. Interestingly, we identified the genes of the biosynthetic gene clusters for zearalenone and T-toxin in all 12 genomes of the isolates from the U.S., yet they were not present in the genome of the rubber isolate. The presence of different T-toxin genes varied among the 12 genomes depending on the host of origin; however, all 4 isolates from cotton contained the 9 genes identified as being involved in T-toxin production in Bipolaris maydis. In C. cassiicola, the T-toxin genes showed synteny with B. maydis; however, they were clustered in a single locus. Studies are underway to determine if C. cassiicola isolates from the three host specialized populations causing epidemics synthesize T-toxin and if it is involved in pathogenicity or virulence. Knowledge of the evolution and variation in necrotrophic effectors of host specialized populations is critical in understanding the genetic basis of specificity and disease emergence of C. cassiicola causing target spot of cotton, soybean, and tomato in the southeastern U.S.

Abstract

The evolutionary history of Fungi is still largely unknown. In this era of genomics, we are no longer limited by the amount of data available to resolve many of their relationships and generate new knowledge. Agaricales is the largest order of mushroom-forming Fungi. The suborder Agaricineae, containing mainly the brown and darked spored Agaricales, was recently shown to be monophyletic. However, the relationships within the suborder remain still largely unresolved. The group includes many important ectomycorrhizal and saprotrophic fungi, as well as edible and commercially relevant mushrooms, such as species of Agaricus. The aim of this study was to generate a robust and well-supported phylogeny of the suborder using genome-wide DNA sequence data. Shallow whole genome sequencing was used to create sequence data of 26 species of Agaricineae. In addition, genomic data of 11 previously published species was obtained from GenBank and JGI databases. Together, these 37 species cover all major families of the group. Selected based on previous studies, 211 single copy genes were extracted from the dataset and used for phylogenomic analysis. Previously published sequence data (ITS, nrLSU, nrSSU, RPB1, RPB2, TEF1) of 250 species was combined with the genomic dataset to produce the most extensive phylogeny of the group up to date. Our results will enable a more stable classification of the group. They will also bring knowledge on the evolution of mycorrhizal and saprotrophic lifestyles within the group. Other evolutionary patterns will also be discussed.

Abstract

Abstract

Bridging the knowledge gap between the approximately 100,000 described fungal species and the estimated 5 million total fungal species will require novel approaches for studying fungi. One major challenge is that many fungal species have not been isolated into pure culture, yet these uncultured species represent most of the observed diversity in environmental DNA amplicon surveys. This issue is exacerbated in the early-diverging fungal lineages, which comprise numerous biotrophic and generally microscopic groups. Recent advances in whole genome sequencing from single cells promise to overcome major challenges in analyzing the genetic makeup of this unknown diversity at a high throughput scale by eliminating bottlenecks imposed by cultivation requirements and workflows. Here we expand our understanding of uncultured lineages of fungi by using our newly developed single-cell genome sequencing pipeline to analyze the genomes of eight uncultured fungal species, seven of which belong to early-diverging lineages. We show that although there is a large variation in genome assembly and gene space recovery (6-88%) from each single amplified genome (SAG), combining data of multiple SAGs from the same species yields estimated genome recoveries of at least 90%. Using even incomplete genomes derived from individual single cells, our phylogenomic analyses provide robust placement for these unsampled lineages on the fungal tree of life, including the previously difficult to place lineages such as Dimargaris cristalligena and Blyttiomyces helicus. Analysis of genomes from single cells allows us to detect polymorphic nucleotides as heterozygous sites and to infer that multiple early-diverging species and the ancestor of fungi was likely diploid. Nearly complete single-cell genomes facilitated comparative genomic analyses, such as investigation of common metabolic deficiencies and characterization of mycoparasitism-related gene family expansions. Additionally, we discovered the first known instance of hydrophobins outside of the Dikarya in the chytrid Caulochytrium protostelioides. These results show that single-cell genomics holds great promise in facilitating fungal phylogenomics, genetically exploring cryptic biology, characterizing nutritional modes and ecological diversity, and discovering novel genes.