Batrachochytrium salamandrivorans

An Martel, University of Ghent, provided the micrograph of B. salamandrivorans, in which (left) Bsal sporangia in mTGhL media develop discharge tubes (arrow) to release zoospores, and (right) a scanning electron microscopic image of Bsal with rhizoids. Duncan Wilson and Matthew Fisher provided valuable comments.Peer reviewedPostprin

Synima : a Synteny imaging tool for annotated genome assemblies

Acknowledgements I would like to thank Chris Desjardins and Brian Haas for assistance and contributions to the ortholog prediction code and pipeline, and José Muñoz and anonymous reviewer 1 for code testing. Funding This work was supported by an MIT / Wellcome Trust Fellowship. Availability of data and materials Synima is open source and freely available from https://github.com/rhysf/ Synima under the MIT License. The download includes all example data presented in this manuscript.Peer reviewedPublisher PD

Nine Things Genomics Can Tell Us About Candida auris

FUNDING RF was supported by MRC grant MR/N006364/2 and a Wellcome Trust Seed Award (215239/Z/19/Z). ACKNOWLEDGMENTS We would like to give thanks to Carolina Coelho for helpful discussions and assistance with Figure 1 and Jose Muñoz for valuable feedback on the manuscript.Peer reviewedPublisher PD

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

Funding: R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study.Peer reviewedPublisher PD

Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen

Data deposition: The sequence reported in this paper has been deposited in the NCBI Sequence Read Archive, https://www.ncbi.nlm.nih.gov/bioproject (BioProject ID PRJNA345600). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1806002115/-/DCSupplemental.Peer reviewedPublisher PD

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity

This project was funded by the UK Natural Environmental Research Council (NERC) grant NE/E006701/1, the European Research Council (ERC) grant 260801-BIG_IDEA, the Swiss National Science Foundation grant 31-125099 and the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity (http://www.bd-maps.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii

Emerging fungal pathogens cause an expanding burden of disease across the animal kingdom, including a rise in morbidity and mortality in humans. Yet, we currently have only a limited repertoire of available therapeutic interventions. A greater understanding of the mechanisms of fungal virulence and of the emergence of hypervirulence within species is therefore needed for new treatments and mitigation efforts. For example, over the past decade, an unusual lineage of Cryptococcus gattii, which was first detected on Vancouver Island, has spread to the Canadian mainland and the Pacific Northwest infecting otherwise healthy individuals. The molecular changes that led to the development of this hypervirulent cryptococcal lineage remain unclear. To explore this, we traced the history of similar microevolutionary events that can lead to changes in host range and pathogenicity. Here, we detail fine-resolution mapping of genetic differences between two highly related Cryptococcus gattii VGIIc isolates that differ in their virulence traits (phagocytosis, vomocytosis, macrophage death, mitochondrial tubularization and intracellular proliferation). We identified a small number of single site variants within coding regions that potentially contribute to variations in virulence. We then extended our methods across multiple lineages of C. gattii to study how selection is acting on key virulence genes within different lineages. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’

MARDy : Mycology Antifungal Resistance Database

J.R. was supported by an Antimicrobial Research Collaborative (ARC) early career research fellowship, Imperial College London (RSRO_54990). T.S. and J.M.G.S. were supported by a Natural Environment Research Council grant awarded to MCF (NE/P001165/1).Peer reviewedPublisher PD

Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways

We thank Jose Munoz for his input on the analysis of the mouse RNA-seq enrichment. R.A.F. was supported by a Wellcome Trust-Massachusetts Institute of Technology (MIT) Postdoctoral Fellowship. M.C.F. and J.R. were supported by Medical Research Council grant MR/K000373/1. R.C.M. is supported by a Wolfson Royal Society Research Merit Award and by funding from the European Research Council under the European Union’s Seventh Framework Program (FP/2007-2013)/ERC (grant agreement no. 614562). This work was funded in part by NIAID grant U19AI110818 to the Broad Institute.Peer reviewedPublisher PD

Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

We acknowledge the Broad Institute Sequencing Platform and Imperial College London for generating the DNA and RNA sequence described here. Financial support was provided by a UK Natural Environmental Research Council (NERC NE/K012509/1) grant to MCF, a Wellcome Trust Fellowship to RF, a Morris Animal Foundation grant to FP, and by the National Human Genome Research Institute grant number U54HG003067 to the Broad Institute. E.V. is supported by the Research Foundation Flanders (FWO grant 12E6616N).Peer reviewedPublisher PD