Welcome to IMC 2018 International Mycological Congress
Conference Calendar
Single cell genomics leads us to a better understanding of the evolution of Arbuscular Mycorrhizal Fungi
- M. Montoliu-Nerin
- C. Bergin
- B. Ellis
- H. Johannesson
- A. Rosling
Abstract
Abstract
Arbuscular Mycorrhizal Fungi (AMF) form symbiotic interactions with over 80% of the land plants. Despite this wide-spread interaction, little is known about the biology of the AMF. The study of AMF has been challenging because of the difficulties in obtaining clean and efficient cultures for DNA extraction. Up-to-date, only one species has been sequenced, and multiple questions remain unsolved, including their life cycle, karyosis, and genomic signatures of their long co-evolution with host plants. We have adapted the method of single cell genomics to obtain genomic data from single nuclei of AMF species that were never studied before. Single spores are crushed and nuclei are stained and isolated individually using the Fluorescence-activated Cell Sorting (FACS). Then, multiple nuclei are amplified and sequenced with Illumina. Several new assemblies are being finalized and I will be presenting comparative genomics results.
Endogonales genomes reveal imprints of ectomycorrhizal lifestyle
- Y. Chang
- A. Desirò
- G. Bonito
- I. Grigoriev
- A. Clum
- A. Lipzen
- J. Spatafora
Abstract
Abstract
Endogonales (Mucoromycotina) is the only known non-Dikarya ectomycorrhizal (ECM) order of fungi, representing one or multiple origins of the ECM lifestyle outside Dikaryon. Recent discovery of the mycorrhizal association between Endogonales fungi and liverworts and hornworts has led to the hypothesis that Endogonales were one of the earliest mycorrhizal partners with land plants and played an important role in the terrestrialization of land plants. In this study we applied shotgun sequencing to four Endogonales isolates from sporocarp tissue. The metagenomic sequence data was first binned using the combination of oligonucleotide-composition-based and BLAST-based methods. During the binning process we identified a large number of Mollicutes-related endobacteria (MRE) sequences in genome of three isolates, consistent with the observation that many Endogonales species harbor MREs. The sizes of the four Endogonales genomes vary from 90 megabases (MB) to 240 MB, much larger than an average fungal genome. The expansion of Endogonales genome size is due to extensive proliferation of transposable elements, which has been observed in many other ECM genomes. In addition, like most ECM fungi, Endogonales has low diversity and low copy numbers of genes coding plant-cell-wall-degrading-enzymes (PCWDEs) in its genome. This is consistent with the notion that ECM lifestyle requires small number of PCWDEs to avoid damaging host plant cells and eliciting host plant defense. Our dating analysis estimated that Endogonales originated in lower Cretaceous, much later than the origin of Glomyeromycotina and the origin of land plants, suggesting that Endogonales were unlikely the first mycorrhizal partner of land plants and that association between Endogonales and plants was established later in evolutionary history of land plants.
Genome assembly of the fungus Leucoagaricus gongylophorus cultivated by the ant Atta colombica using long-read MinION sequences
- P. Kooij
Abstract
Abstract
Assembling heterogenous (two very different sets of chromosomes) or polyploid (more than two sets of chromosomes) genomes can be challenging, but in a fast-developing world, new techniques and software are regularly developed. Leaf-cutting ants cultivate a polyploid fungus with an average of 7 different genomes which has proven to be difficult to assemble using regular short-read genome sequencing. In this study, I used the Oxford Nanopore Technologies MinION to produce long-read sequences. I then used a series of different software packages to assemble genomes from long-read sequences (CANU and Nanopolish) as well as software to deal with heterogeneous and polyploid species (Redundans). The quality of the assemblies was tested by extracting a core set of single-copy genes using BUSCO. With this, I developed a pipeline to assemble fungal genomes accurately using long-read sequences. The resulting genome assembly is an improvement of the one currently available and gives new insights into this intriguing mutualism between ants and fungi. Furthermore, I was able to fully assemble the fungal mitochondrial genome with a high coverage (±4000X), which can be used to both understand the mechanistic of this fungus, but which can also be used for more accurate phylogenetic analyses. In conclusion, I was able to show cost-efficient methods and a pipeline to accurately assemble fungal genomes, that can be used for a wide variety of analyses.
scgid, a bioinformatic tool for scaffold binning and genome prediction from metagenomic sequencing libraries
- K. Amses
- T. James
Abstract
Abstract
A kind of dark matter within the kingdom, “uncultured” fungi remain largely inaccessible in the context of genomic studies in the age of next-generation sequencing. Resistance to axenic culture techniques makes acquisition of sufficient input tissues for whole-genome sequencing a near impossible endeavor for these fungi. To circumvent these obstacles, extraction techniques that incorporate non-specific amplification steps can be used to generate sufficient final DNA concentrations from low input materials (single-cell genomics). The nature of these non-specific amplification steps makes sequencing libraries generated in this way especially prone to contamination originating from either the environment or the laboratory. There are a variety of post hoc bioinformatic methods available to attempt to eliminate contamination from these sequencing libraries. All of these methods involve binning of genome assembly scaffolds into target and non-target bins, which can be used to call a final genome draft. Interestingly, when confronted with the same data set, each of these different methods can call a very different final genome. This ambiguity and disagreement among methods seems to be dataset-dependent in such a way that no one method is always conservative or always liberal in its inclusion or exclusion of a scaffold from the final genome draft. This issue poses a major issue to the identification of high-confidence final genomes of uncultured fungi and hinders downstream analyses incorporating them. To address this, we propose the use of a consensus-based approach leveraged toward determining which final bin a scaffold belongs in. Building upon past work and theory developed and implemented by other authors, the python-based bioinformatic tool scgid uses three distinct binning methods that bin scaffolds based on independent sets of characteristics. From these three drafts, a final, high-confidence consensus genome draft can be called by majority rule, minimizing contamination while maximizing inclusion of target sequences at the intersection of all three independent methods. This tool should prove useful to genome sequencing efforts in uncultured organisms across the tree of life where the goal is extraction of a high-confidence genome from moderately metagenomic sequencing libraries.
Era of the living dead: Resurrecting fungal genomes from fungaria with metagenomics
- B. Dentinger
- P. Avis
- T. Niskanen
- K. Liimatainen
- L. Suz
Abstract
Abstract
Fungaria are the most mycologically diverse places on the planet and harbor a wealth of potential genetic data for phylogenetics, comparative genomics, taxonomy, and nomenclature. Yet, little molecular exploitation of this diversity has been realized. Until recently, this lack of development was due to technical challenges in harvesting genetic data from poorly preserved specimens where nucleic acids suffer from mild to severe degradation. High throughput DNA sequencing technologies that utilize short fragments has, in theory, largely overcome this technical impediment, yet progress in liberating these molecules from fungaria has been slow. Here, we show how shotgun sequencing of fungarium specimens, including type specimens from Charles Peck and others, is essentially a metagenomics problem where whole genome coverage of target taxa can yield profound information to generate robust phylogenetic hypotheses, anchor scientific names, and possibly provide high resolution information for comparative genomics, such as biosynthetic gene clusters. The fungarium genomics era has the potential to solve myriad puzzles resulting from our current state of knowledge of fungal diversity, including the enduring predicament posed by application of old names through type authentication, establishing its quintessence in contemporary science by breathing new life into the ancient and recent dead.
Metagenomic strategies for inferring biological aspects of fungal endosymbiont systems
- J. Uehling
- J. Vélez
- F. Dietrich
- C. Schadt
- J. Labbé
- G. Bonito
- R. Vilgalys
Abstract
Abstract
As we approach our goal of sequencing 1,000 fungal genomes it is becoming evident we will need to include DNAs from sporocarps, fungi in obligate symbioses, and fungal taxa with bacterial endosymbionts to sample genomic diversity across the Kingdom. These systems represent unique opportunities to study fungal evolution, and to develop comparative ‘–omic’ pipelines that lend insights to hypotheses about how symbioses are initiated and evolve. Obligate, long-term, co-evolved fungal endosymbionts and their hosts are one example of a study system poised to propel evolutionary questions in mycology in new directions. Our research group has been investigating fungal bacterial symbioses using Mortierella elongata (Mortierellomycotina, Mucoromycota) and bacterial endosymbiont Mycoavidus cysteinexigens (Burkholderiales). However, fungal endosymbiont interactions and other fungal symbioses are challenging to study for the following reasons. First, genomes must be extracted from metagenomic sequencing efforts requiring novel pipelines and creative quality checks to avoid assembly artifacts. Second, several fungal endosymbiont hosts belong to the former zygomycetes, a group of early diverging fungi lacking homology to current fungal model genetic systems, driving need for next generation annotation strategies and pipelines. Lastly, deriving testable, functional hypotheses about symbiotic interaction mechanisms from these complex data sets will require innovative approaches. We have developed metagenome sequencing and computational sorting, transcriptomics, metabolomics, and volatomics for studying fungal endosymbiont interaction dynamics in the Mortierella-Mycoavidus system. Challenges and insights from these endeavors will be discussed.