882 research outputs found
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
No full textAspergillus fumigatus is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on de novo assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in A. fumigatus. We provide evidence for three distinct populations of A. fumigatus, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, A. fumigatus demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.
Accompanying manuscript is available as preprint at https://dx.doi.org/10.1101/2021.12.12.472145
Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145This is an update from v2 of this dataset, it add additional supplemental files related to population structure, CAZY analysis and reflects updated datasets to match the v3 of the manuscript
DNA sequence databases
No full textThe ability to sequence the DNA of an organism has become one of the most important tools in modern biological research. Beginning as a manual process, where DNA was sequenced a few tens or hundreds of nucleotides at a time, DNA sequencing is now performed by high throughput sequencing machines, with billions of bases of DNA being sequenced daily around the world. The recent development of next generation sequencing technology increases the throughput of sequence production many fold and reduces costs by orders of magnitude. This will eventually enable the sequencing of the whole genome of an individual for under 1,000 dollars. However, mechanisms for sharing and analysing this data, and for the efficient storage of the data, will become more critical as the amount of data being collected grows. Most importantly for biologists around the world, the analysis of this data will depend on the quality of the sequence data and annotations which are maintained in the public databases. In this chapter we will give an overview of sequencing technology as it has changed over time, including some of the new technologies that will enable the sequencing of personal genomes. We then discuss the public DNA databases which collect, check, and publish DNA sequences from around the world. Finally we describe how to access this data
stajichlab/Hortaea_werneckii: Data freeze associated with Gostincar et al 2021.
No full textDataset frozen in accompany with previous analysis and publication from Gostinčar C, Stajich JE, Kejžar A, Sinha S, Nislow C, Lenassi M, Gunde-Cimerman N. Seven Years at High Salinity-Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii. J Fungi (Basel). 2021 Sep 4;7(9):723. doi: 10.3390/jof7090723. PMID: 34575761; PMCID: PMC8468603.
Not all analyses here were part of final publication but this represents some of the work we did in exploring the datasets
Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches
No full textMost fungi from the Mucoromycotina lineage occur in ecosystems as saprobes, although some species are phytopathogens or may induce human mycosis. Mucoromycotina represent early diverging models that are most valuable for understanding fungal evolution. Here we reveal the uniqueness of the cell wall structure of the Mucoromycotina Rhizopus oryzae and Phycomyces blakesleeanus compared with the better characterized cell wall of the ascomycete Neurospora crassa. We have analysed the corresponding polysaccharide biosynthetic and modifying pathways, and highlight their evolutionary features and higher complexity in terms of gene copy numbers compared with species from other lineages. This work uncovers the presence in Mucoromycotina of abundant fucose-based polysaccharides similar to algal fucoidans. These unexpected polymers are associated with unusually low amounts of glucans and a higher proportion of chitin compared with N. crassa. The specific structural features are supported by the identification of genes potentially involved in the corresponding metabolic pathways. Phylogenomic analyses of genes encoding carbohydrate synthases, polysaccharide modifying enzymes and enzymes involved in nucleotide-sugar formation provide evidence for duplication events during evolution of cell wall metabolism in fungi. Altogether, the data highlight the specificity of Mucoromycotina cell walls and pave the way for a finer understanding of their metabolism.Hugo Mélida, Divya Sain, Jason E. Stajich, Vincent Bulon
hyphaltip/subopt-kaks: Release 1.0.0 of subopt-kaks
No full text<p>This code has been stable / in-place since ~2006 and represents work from Jason Stajich's PhD thesis exploring how variation in pairwise suboptimal alignment impact estimations of Ka and Ks for molecular evolution distances.</p>
<p>By far the most useful aspect is rapid pairwise implementation of YN00 estimation of Ka and Ks from alignments into simple tabular output to support quick prototyping and scans of molecular divergence. See yn00_cds_prealigned for that main code as well as yn00_cds_optimal for pairwise alignment calculation from unaligned CDS sequence.</p>
Taxonomic vs genomic fungi
No full textSupplementary files for
Taxonomic vs genomic fungi: contrasting evolutionary loss of ancestral genomic heritage and punctuated emergence of fungal novelties
Zsolt Merényi Krisztina Krizsán Neha Sahu Xiao-Bin Liu Balázs Bálint Jason Stajich Joseph W. Spatafora László G. Nagy</p
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Biological Soil Crusts Microbiomes: An Exploration and Investigation of Factors Influencing Biocrust Microbial Communities in Mojave Desert, USA
No full textBiological soil crusts (biocrusts) are major components in the dryland environment. They contain diverse microbial communities with crucial functions to dryland ecosystems. However, very little is known about these microorganisms because the biocrusts are defined by their external morphology which oftentimes neglect these unseen world. To better understand biocrusts microbial communities, extensive and integrated microbial research (external morphology and microorganisms) on biocrust is needed. Therefore, in my dissertation work I aimed to 1) summarize previous and current research, and identify knowledge gaps about biocrust microbes to provide baseline understanding about biocrust microorganisms, 2) identify key factors that influenced the biocrust microbes from three domains of life (archaea, bacteria, and fungi), and 3) to further expand our understanding about temporal/seasonal effect on these microorganisms. We employed amplicon-based metabarcoding sequencing to investigate biocrusts microbial communities. In chapter 2, our results showed that biocrusts microorganism are diverse and we are only at the beginning of biocrust microbes investigation because many microorganisms cannot be identified which could be new to science. We have modified sequencing protocols that work well with JTNP biocrusts and a baseline knowledge about biocrust microbes was established. Then, in chapter 3, we expanded our study to cover the Mojave Desert. To test our hypotheses that geography, soil depth, and crust types influenced biocrust microbial communities, 5 common biocrust types samples were collected from 4 sites across the Mojave desert. The results showed that 1) Biocrust in central Mojave were distinct from southern Mojave site, 2) biocrust surface harbored different microorganisms from subsurface soil, and 3) crust types displayed different community signatures. Moreover, microbials hubs species that connect biocrust microbes together were also identified. Lastly, chapter 4 concluded this dissertation by improving our baseline knowledge documenting how these microbial communities changes over the year and investigate how weather patterns that influenced these changes in microbial communities. We hypothesized, biocrust microbial communities were dynamic and weather including temperature, precipitation, wind speed, atmospheric pressure, humidity, and dew point influenced biocrust microbial composition. These findings not only improve our baseline understandings about biocrust microorganisms but also provide essential information for future biocrust management and conservation
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Transposable Element Dynamics in Genomes of Giant Insect - Killing Fungi of the Entomophthoraceae
No full textFungal family Entomophthoraceae that are obligate pathogens of insects have massive genomes, some exceeding 1 Gb. They are largely expanded by transposable elements (TEs), but the reason and impact of TE driven genome expansion remains poorly understood. This study investigates TE - mediated genome expansion, active TE families, and the mechanisms of TE silencing in these early diverging fungi. I used Extensive de-novo TE Annotator (EDTA) for de novo TE discovery and characterization in this study. I identified LTR/Ty3 retrotransposons as the primary contributors to genome expansion, with the largest TE families proliferating after species diversification. While Entomophthora muscae exhibits a compartmentalized genome distinct from the classic "two-speed genome" model, no evidence of a RIP-like mutation system for TE silencing was detected for Entomophthoraceae genomes. Notably, two active MITE families and their associated autonomous elements were identified in Entomophaga maimaiga, with insertion preferences near genes consistent with other MITE families. This study provides critical insights into TE-driven genome expansion in Entomophthoraceae, advances our understanding of their evolutionary history, and establishes a framework for characterizing active TEs in early diverging fungi
Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling Three Representative Locations of the Victoria Land
No full textThe endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and functionality at the dry limits of life. To assure a reliable estimation of microbial diversity, proper sampling must be planned in order to avoid the necessity of re-sampling as reaching these remote locations is risky and requires tremendous logistical and economical efforts. In this study, we seek to determine the minimum number of samples for uncovering comprehensive bacterial and fungal diversity, comparing communities in strict vicinity to each other. We selected three different locations of the Victoria Land (Continental Antarctica) at different altitudes and showing sandstone outcrops of a diverse nature and origin-Battleship promontory (834 m above sea level (a.s.l.), Southern VL), Trio Nunatak (1,470 m a.s.l., Northern VL) and Mt New Zealand (3,100 m a.s.l., Northern VL). Overall, we found that a wider sampling would be required to capture the whole amplitude of microbial diversity, particularly in Northern VL. We concluded that the inhomogeneity of the rock matrix and the stronger environmental pressure at higher altitudes may force the communities to a higher local diversification
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An ‘Omics Investigation into the Effects of Aluminum Toxicity on Arabidopsis Thaliana
No full textAluminum (Al) toxicity is a global problem that leads to stoppage of root growth, overall smaller plant size and lower crop yields. Previous research has shown the molecular response of plants to Al toxicity occurs through a DNA damage response pathway involving ATR and SOG1 genes. To explore this phenomenon further both transcriptomic and genomic experiments were performed using Arabidopsis Thaliana. The goal of the transcriptomics was to determine a gene or suite of genes that were deferentially expressed with Al3+ exposure that could potentially confer Al tolerance to crop plants. While a companion genomics study aimed to understand what type of genomic damage was occurring following Al exposure. Arabidopsis seedlings were grown on gel soaked media plates in the absences or presence of Al3+, before nucleic acids were harvested for Illumina short read sequencing. Transcriptionally, a suite of genes that included known Al response factors and some novel genes were identified using a cut off of 2 fold change and a false discover rate of 1%, 10 of the genes had their expression validated using quantitative real time PCR. In addition, it was identified genetically that Al toxicity leads to the generation of one and two base pair insertions and deletions, which were determined to be statistically significant. With this knowledge future experiments can be performed with the promise of finding the molecular critical to responding to Al exposure and how to use this response to confer Al tolerance to crop plants. Such experiments should include testing Arabidopsis mutants that have reactive oxygen species related genes knocked out or overexpressed to evaluate the level of genomic damage in the presence Al3+. Additionally, genes identified from this transcriptional study should have their expression modified to further understand their role in Al toxicity. Pathway interaction studies with these factors could highlight the full molecular pathway of the plants response to Al exposure
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