Welcome to IMC 2018 International Mycological Congress
Shared versus independent losses: evolutionary consequences of intracellular parasitism in cryptic Fungi
- C. Quandt
- T. James
Phylogenomic analyses have suggested that a clade comprising eukaryotic parasites with the smallest known genomes, Microsporidia, and the phylum known primarily from environmental sequences, Rozellomycota, are at the base of the fungal phylogeny. However, the ecological and genetic similarities between these distant relatives remains unclear. Recently we compared genome data of Rozellomycota and Microsporidia with the newly acquired nuclear and mitochondrial genomes of Paramicrosporidium saccamoebae – an intranuclear parasite of amoebae. Our analyses demonstrate that Microsporidia are nested within Rozellomycota, which forms a paraphyletic clade. Comparative analysis revealed that P. saccamoebae shares more gene content with distantly related Fungi than with its closest relatives, suggesting that genome evolution in Rozellomycota and Microsporidia has been affected by repeated and independent gene losses, possibly as a result of variation in parasitic strategies (e.g. host and subcellular localization) or due to multiple transitions to parasitism. To understand if this represents a larger pattern of independent gene loss within the clade, we have sequenced the genomes of new rozellids and another amoeba-parasite that previous work suggests may be the closest relative to Microsporidia. Here we will explore the variation in gene content and genome evolution within this clade of intracellular parasites.
Using codon usage bias to predict ecologically adaptive metabolic pathways in the budding yeast subphylum
- A. Labella
- D. Opulente
- C. Hittinger
- A. Rokas
Since diverging about a half-a-billion years ago, the 1,000+ yeast species of the subphylum Saccharomycotina have diversified into every biome on Earth. The diversity of yeast ecological adaptation is underpinned by their ability to utilize a wide range of substrates and grow in a variety of environments. Traditionally, metabolic pathways that are key for yeast ecological adaptation have been identified through functional experiments in the laboratory, statistical analysis of associations between traits and environments, and by examining signatures of selection in the genes encoding metabolic enzymes. One genomic signature that has proven especially powerful at predicting gene activity, but has yet to be widely employed in evolutionary ecological research, is codon usage bias or the differential use of synonymous codons within and between genomes. The strongest driver of genome-wide codon usage bias patterns is G/C mutational bias. Codon usage bias at the level of individual genes, however, is a consequence of selection for translational efficiency, and therefore, gene level bias is strongly associated with gene expression. We expect that highly expressed genes will show codon usage bias in favor of optimally translated codons and that networks of co-expressed genes will show bias in favor of the same set of codons. In this work, we use species-specific gene-based estimates of codon usage bias (as a proxy for genes’ expression levels) to predict metabolic pathways that are highly active across the genomes of 332 budding yeast species. These active metabolic pathways are then compared to the known habitat features of these 332 budding yeast species to identify significant associations between highly active metabolic pathways and habitat features. In my presentation, I will report the results of these analyses. Identification of significant associations between metabolic activity predicted by codon usage bias analysis and habitat features will provide insight into which metabolic capabilities may be responsible for adaptation to specific environments. More broadly, this work also sheds light on the ability of codon usage bias to be more broadly used to predict ecologically relevant genes and pathways in other microbes--especially those that are currently unculturable.
The role of gene flow in rapid adaptive evolution of fungal plant pathogens: a comparative population genomics study
- A. Feurtey
- D. Stevens
- C. Eschenbrenner
- W. Stephan
- E. Stukenbrock
Antagonistic co-evolution between pathogens and their hosts can drive rapid adaptive changes in both partners. Pathogens exert a strong selection pressure on their hosts, in particular on immune defense genes. At the same time, host resistance can be overcome in the pathogen evolving to escape host recognition or to suppress host defenses. The genetic innovations allowing rapid adaptation in this evolutionary “arms-race” can have various origins including mutational events, sexual recombination and gene flow. Genome-based studies of fungal pathogens have revealed a frequent contribution of inter-specific gene exchange in rapid evolution. We used a population genomics approach based on de novo assemblies of genomes and whole genome alignments to characterize the distribution of highly variable regions in the fungal wheat pathogen Zymoseptoria tritici. These regions are found throughout the genome, comprise around 5% of the total genome size and overlap with 600 predicted coding sequences. We performed window based phylogenetic analyses align the genome alignment and show that the highly variable regions overlap with regions of showing signature of past interspecific hybridization events. We detect a similar pattern in the closely related wild grass pathogen, Zymoseptoria ardabiliae, and some hybridization events have involve these two species. Overall, our results demonstrate a significant impact of frequent interspecific hybridization on the genome evolution of this important wheat pathogen. We speculate that gene flow act to fuel arms race evolution of Z. tritici with its host.
Coccidioidomycosis in the surrounding landmasses of the Caribbean Sea is caused by cryptic Coccidioides posadasii populations
- B. Barker
- M. Teixeira
- P. Alvarado
- G. Thompson
- E. Arathon
- C. Canteros
Coccidioides posadasiicauses coccidioidomycosis in arid regions of the Americas. C. posadasiiis comprised of at least two populations; Arizona (AZ) and Texas/Mexico/South America (TXMXSA). The exact range of C. posadasiiin Central and South America is undetermined for many reasons. For one, the disease is sub-notified to local health departments. Second, fewer than 1,000 total cases across the region have been reported. The Caribbean region is bordered by the Caribbean Sea, and the surrounding continental landscape and islands may play an important role in the dispersion of C. posadasiithrough Mexico, Guatemala and Venezuela. To define the distribution of C. posadasiipopulations in Central and South America, we sequenced the genomes of 6 clinical isolates from Venezuela, 1 from Argentina, 2 from Mexico, 1 from Texas and 1 from Florida. References were assembled using the Unmanned Genome Assembly Pipeline using SPAdes as well the Pilon toolkit. Weincorporated 52 published genomes from C. posadasiito identify the genetic background of newly sequenced strains and develop hypotheses regarding the dispersion into Central and South America.Maximum Likelihood methods implemented in IQ-TREE software using jModelTest for model selection and 1,000 ultrafast bootstraps with Shimodaira-Hasegawa-like approximate likelihood ratio test were performed for branch confidence. The genealogical concordance level was tested using the Bayesian concordance analysis implemented in the BUCKy. To avoid linkage disequilibrium effect, the SNP matrix was assessed in 2500bp blocks. Posterior tree distribution of each locus was individually tested via MrBayes under GTR nucleotide substitution model. SNP matrices were run using two independent Markov Chain Monte Carlo simulations and four chains for 10 million generations with samples collected every 1,000 generations. Tracer was used to check convergence between the two chains and individual loci. Time-scaled phylogenies were calculated for timing analyses in BEAST. Trees topologies were visualized using FigTree. Comparative phylogenomic analyses reveal that clinical strains from Guatemala and Venezuela are genetically isolated from the well described populations AZ and TXMXSA, whereas the new Texan, Mexican and Argentinian isolates cluster with TXMXSA as expected. Analysis indicates that limited gene flow exists between Guatemala and AZ populations, whereas we observe nearly complete reproductive isolation from both AZ and TXMXSA among the newly sequenced Venezuela isolates. Interestingly, the isolate from a Florida patient was paraphyletic to the Venezuela/Guatemala cluster. Based on these observations, we propose new patterns of dispersion and endemicity through Central and South America. We provide strong evidence that the South American continent was colonized by at least two ancestral populations: one by a TXMXSA ancestral genotype, and the second by a Guatemalan ancestral genotype. Isolates from Brazil, Argentina and Paraguay cluster within the TXMXSA cluster whereas the Venezuelan clade shares a common ancestor with the Guatemalan cluster and together forms a newly designated “Caribbean” population, including the isolate from Florida, which is distinct from either AZ or TXMXSA. We propose that the Venezuela lineage was purified during migration through Central America to the semi-arid regions of the Paraguanápeninsula and the depression valleys of Lara and Falcon states.
Genome-wide survey for understanding genetic basis of morphological evolution of septal pore cap in Agaricomycetes
- T. Iizuka
- K. Ikeo
Understanding genetic basis of morphological evolution is essential for clarifying the evolutionary history of fungi. To understand the evolution of Agaricomycetes, morphological character of septal pore cap (SPC) is one of the key characters to distinguish taxonomy. In our study, we are focusing three phenotypes of SPC (vesiculate, imperforate and perforate) and searched candidate causal mutation of the differences of SPC types from fungal genome sequences. Among these three phenotypes, vesiculate SPC is known as the most ancestral characters. After the emergence of imperforate SPC from vesiculate SPC, perforate SPC had been evolved from imperforate SPC at multiple times independently (morphological independent evolution). The objective of this research is detecting mutation correlated with morphological evolution of these three types of SPC in amino acid sequence level. As the first step, for detecting the gene correlated with the evolution from imperforate SPC to perforate SPC, we searched genes that has parallel substitutions correlated with the emergence of perforate SPC from imperfotrate SPC against orthologous gene datasets of 12 fungal genomes. When genes were clustered by SPC type rather than species phylogeny by phylogenetic analysis from each orthologs, the genes were extracted as candidate causal genes. By using these genes, we searched SPC-type specific sites that show differences of amino acid residue depending on the difference of SPC types. We also checked whether the substitution had been derived in the exact ancestral brunch that is reasonable to assume as the period of emergence of perforate SPC by ancestral sequences reconstruction. For detecting the gene correlated with the evolution from vesiculate SPC to imperforate SPC, BLAST search against vesiculate type species was conducted to know gene present/absent pattern of detected gene. We detected spc33 as a gene correlated to the morphological evolution of SPC. Amino acid substitutions D254E, K357R, V359I and P402R were observed during morphological independent evolution from imperforate type species to perforate type species in both lineages. When we checked each sites of multiple alignment of spc33, we found K357R and M/V359I are remained such differences in extant species. Therefore, same genetic changes were detected from the independent emergence of perforate SPC. The results of BLAST search showed that spc33 was observed only from imperforate type species and perforate type species. Vesiculate type species and any other organisms did not have spc33 homologs. In conclusion, correlated evolutionary event in amino acid sequences of spc33 had been occurred during both the evolution from vesiculate SPC to imperforate SPC and the evolution from imperforate SPC to perforate SPC.
Multiple evolutionary origins lead to diversity in the metabolic profiles of ambrosia fungi
- Y. Huang
- J. Skelton
- J. Hulcr
Ambrosia fungi are an ecological assemblage of species cultivated by ambrosia beetles in their gallery as required nutrient sources. This nutritional mutualistic relationship with beetles has evolved at least 7 times in Dikarya (Ascomycota and Basidiomycota). However, whether convergence in ecology led to convergent metabolism in ambrosia fungi is still unknown. We compared the assimilation of 190 carbon sources in five independent lineages of ambrosia fungi and closely related, non-ambrosial species. These repeated comparisons, and the use of variation partitioning to separate the effects of phylogeny and ecology, enabled us to assess functional convergence versus phylogenetic divergence in the metabolic diversity of ambrosia fungi. Our results revealed no convergence in carbon utilization capacities among ambrosia fungi. Instead, metabolic variation among fungi was largely explained by phylogenetic relationships. In addition, the range of carbon usage was as diverse in ambrosia fungi as in non-ambrosial species. Our results demonstrate that carbon metabolism of each ambrosia fungus is determined by its inherited metabolism, rather by the transition towards symbiosis. In contrast to other fungus-farming systems of termites and attine ants, the fungal symbionts of ambrosia beetles are functionally diverse, which reflects their independent evolutionary origins.