Fungi are very important with regard to the economy and ecology. They decompose dead organic matter and recycle nutrients in various ecosystems, including soil. Some fungi, such as mushrooms and yeasts, are used for food and medicine. Others can cause human and plant diseases. More than a million species in the kingdom Fungi cover more than a billion years of evolutionary history. The evolutionary innovations encoded in their genomes can be deciphered using genomics.
The first eukaryotic genome to be sequenced was that of the fungus Saccharomyces cerevisiae, which dramatically changed the biological sciences and led to the development of a whole spectrum of new tools and discoveries in genetics and molecular biology. Following this initial genome sequencing, several dozen fungal genomes have been sequenced by the Fungal Genome Initiative, led by the Broad Institute in Cambridge, Massachusetts; these fungi have been predominantly those of medical importance. Fungi are also important for plant health. Some, such as mycorrhizal fungi (that is, fungi that form symbiotic relationships in and on the roots of host plants), help plants to extract nutrients from the soil; others, such as rusts and rots, can kill plants. Most fungi contribute significantly to carbon cycling.
To address questions related to energy and the environment, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has been developing genomic resources and tools to explore fungal diversity at large. To facilitate fungal genomics efforts, JGI has partnered with the scientific community around the world and started several large-scale genomics initiatives. The first of them, the Genomic Encyclopedia of Fungi for Energy and Environment, is focused on the analysis of groups of fungi that are important for growing biomass and converting it into bio-fuels. The second initiative, the 1000 Fungal Genomes Project, aims to explore fungal diversity across the Fungal Tree of Life [the classification of Fungi based on phylogenetic (evolutionary) relationships] and to provide references for studying fungal communities in soil and other ecosystems. The third initiative will provide functional information for the sequenced genes and genomes using the functional genomics of individual fungi and fungal communities.
Using these initiatives, JGI solicits genomics proposals for sequencing and analyzing large amounts of genomic data from researchers around the world to solve various energy and environmental problems. To enable these analyses, JGI has also developed a Web-based fungal genomics resource, MycoCosm, which provides tools to analyze more than 200 fungal genomes and promotes user participation in data submission, annotation, and analysis (see illustration).
Genomic Encyclopedia of Fungi for Energy and Environment
The Genomic Encyclopedia of Fungi for Energy and Environment initiative aims to analyze groups of diverse fungi that share the same traits, lifestyle, secretions, and other features for energy- and environment-related science and applications. The two initial focus areas involve fungi that (1) can positively or negatively affect plant health and bioenergy crops and (2) encode genes, pathways, and other parts that are important for developing efficient biorefineries for biofuel production.
Plant health maintenance is critical for sustainable growth of biofuel feedstocks, and fungi [mutualists, parasites, and other microbial components of the rhizosphere (the soil region subject to the influence of plant roots and characterized by a zone of increased microbiological activity)] can dramatically affect this. Mycorrhizal fungi, for example, enter into symbiotic relationships with plants and effectively extend the host root system toward regions of decaying organic matter to provide nutrients such as nitrogen and phosphorus. Comparison of the first two sequenced genomes of mycorrhizal fungi, the poplar symbiont Laccaria bicolor and the black truffle Tuber melanosporum, has revealed dramatic differences in their gene sets and their interactions with host plants, justifying a more comprehensive study of 25 mycorrhizal fungi. While sequencing of these genomes is in progress, a dozen new plant pathogens from the fungal class of Dothideomycetes have been sequenced and analyzed in the largest comparative study of its kind to date. This study revealed genomic differences and aligned some of them with different strategies of pathogenicity, including the expansion of genes involved in secondary metabolism and plant cell wall degradation in fungi-killing plants (necrotrophs) in comparison to those parasitizing from inside plants (biotrophs). When this is followed by in-depth analyses and functional genomics studies, it should lead toward the development of new methods of controlling the growth of pathogenic fungi and protecting plants from catastrophic events (such as the 1970 epidemic of corn leaf blight, which wiped out the entire corn crops of several states in the United States).
Biorefinery methods convert the biopolymers composing the plant cell wall (lignocellulose) into simple sugars (glucose and xylose) and then into biofuels using fungal strains optimized for large-scale industrial processes. Knowing the enzymes and processes employed by diverse fungi in lignocellulose degradation and sugar fermentation, and also understanding the molecular biology of the strains adopted by industry, are essential for developing robust platforms for biomass-to-biofuel production on an industrial scale. Comparison of the genomes of the white rot fungus Phanerochaete chrysosporium and the brown rot fungus Postia placenta revealed very different mechanisms of lignocellulose degradation for each of them. This led to the sequencing of 30 more wood-decay fungi from the class Agaricomycetes to build the most comprehensive catalog of lignocellulolytic enzymes and reconstruct white and brown rot evolution. Sugars produced by these processes include xylose, which is processed poorly by industrial strains of S. cerevisiae, but efficiently by other yeasts (for example, Pichia stipitis). Comparative genomics of several xylose-fermenting yeasts suggested missing genes, which have been added to S. cerevisiae to enable more complete sugar processing during biomass decomposition. Another way to improve industrial enzyme-producing or sugar-fermenting strains of fungi is to replace them with thermophilic fungi (that is, fungi that thrive at high temperatures). Two of these, Thielavia terrestris and Myceliophthora thermophila, have displayed good biomass decomposition potential at high temperatures and have been sequenced to produce complete chromosomes, which can be used as detailed maps for further genome engineering and strain improvement. The research community will continue to add new chapters of the Encyclopedia to explore a number of different areas—for example, the roles of fungi in ecology, the secrets of endophytes (fungi that live within, but are not necessarily parasitic on, plants) and extremophiles (organisms that live and thrive in environments with extreme conditions), and the potential of fungi for bioremediation (the use of a biological process to clean up a polluted environmental area).
1000 Fungal Genomes
Despite the growing number of fungal genome sequencing projects, sequenced fungi represent only a tiny fraction of the natural fungal diversity created by more than a million different species. The majority of the fungal species in soil or other environments are not characterized and do not have any genome information. They may be a potentially rich source of valuable metabolic pathways and enzyme activities, and there is thus a need for a systematic survey of phylo-genetically diverse genome sequences. To address this need, an international research team, in collaboration with JGI, has embarked on a 5-year project (the 1000 Fungal Genomes Project) to sequence 1000 fungal genomes from across the Fungal Tree of Life. The goal is to fill in gaps in the Fungal Tree of Life by sequencing at least two reference genomes from each of the more than 500 recognized families of Fungi. With several culture collections participating and with growing interest from the entire mycological community, this project aims to provide genomic references to inform research on plant–microbe interactions and environmental metagenomics (the analysis of many genomes simultaneously). The MycoCosm portal provides integrated information for ongoing genome sequencing projects, the list of known families of Fungi, and tools for nominating new species and assigning them to families with no sequenced genomes. Any researcher can nominate fungal species in these families and can send DNA samples to JGI for sequencing and annotation.
Functional genomics of fungal systems
Whereas traditional genomics focuses on genome sequencing and computational analysis of predicted genes, functional genomics should provide experimental data on the function of these genes. There have been revolutionary changes in sequencing technologies, but not as much in the biochemical characterization of genes and proteins, creating a growing gap between the available sets of sequences and functions. However, initiatives such as the Human ENCODE project (which seeks to build a comprehensive parts list of the functional elements in the human genome) give promise of developing high-throughput techniques that could be applicable to fungi and other organisms. These may include new experimental techniques for examining and delineating a number of genomic features [including, for example, interactions of chromatin (the wrapping of the genome into a complex between DNA and proteins); DNA accessibility and structure; modifications of histones (a large class of proteins associated with nucleic acid molecules); transcription factor binding sites; DNA methylation; promoters; and transcriptional silencers].
Sequence-based high-throughput approaches such as transcriptomics (the study of the entire complement of RNA that has been transcribed from DNA in a cell or, more likely, a population of cells) and proteomics (the study of the total protein complement of a cell, a tissue, or an entire organism) have been successfully utilized for many fungi. Large collections of deletion mutants for the model yeast S. cerevisiae and the filamentous fungus Neurospora crassa help in better portraying the role of individual genes (by using resequencing and transcriptomics), and there is a need for further collections to be developed for a significantly larger number of fungi. Transcriptome analysis of systems consisting of an interacting host and fungal pathogens or symbionts can shed light on changes in both and can help provide information on their interactions. Large-scale transcriptomics studies of several pathogen–host and mycorrhizal fungi–host systems are also currently in progress at JGI, along with the N. crassa ENCODE project. Moreover, initial efforts on metatranscriptomics of complex fungal communities (such as soil) could ultimately lead to understanding the interactions in these communities and modeling their responses to environmental changes.
Conclusions
Fungi encode processes that are important for the economy and ecology in their genomes. Dramatic changes in genome sequencing in the last few years have opened the doors to massive genome explorations. To integrate the large amounts of genomics data and to better coordinate the efforts of a large research community, new tools have been developed and several genomic initiatives have been launched at JGI to study large groups of fungi relevant to bioenergy, explore the phylogenetic diversity of fungi at the scale of 1000 genomes, and develop fungal genomics of model systems and microbial communities.
See also: Biomass; Fungal biotechnology; Fungal ecology; Fungal genetics; Fungal genomics; Fungal phylogenetic classification; Fungi; Lignin-degrading fungi; Mushroom; Mycology; Mycorrhizae; Recombinant fungal biotechnology; Yeast
