Publications by year
In Press
Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (In Press). Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians.
Abstract:
Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians
ABSTRACTParasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into sterile culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to interested researchers worldwide as part of the BiodivERsA project RACE – here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been widely applied across at least 5 continents, 23 countries and in 62 amphibian species, and have been successfully used to isolate chytrids in remote field locations. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this important group of emerging fungal pathogens.
Abstract.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (In Press). Genomic basis of multidrug-resistance, mating, and virulence inCandida aurisand related emerging species.
Abstract:
Genomic basis of multidrug-resistance, mating, and virulence inCandida aurisand related emerging species
AbstractCandida aurisis an emergent fungal pathogen of rising public health concern due to increasing reports of outbreaks in healthcare settings and resistance to multiple classes of antifungal drugs. While distantly related to the more common pathogensC. albicansandC. glabrata,C. aurisis closely related to three rarely observed and often multidrug-resistant species,C. haemulonii, C. duobushaemulonii and C. pseudohaemulonii. Here, we generated and analyzed near complete genome assemblies and RNA-Seq-guided gene predictions for isolates from each of the four majorC. aurisclades and forC. haemulonii, C. duobushaemulonii and C. pseudohaemulonii. Our analyses mapped seven chromosomes and revealed chromosomal rearrangements betweenC. aurisclades and related species. We found conservation of genes involved in mating and meiosis and identified bothMTLaandMTLαC. aurisisolates, suggesting the potential for mating between clades. Gene conservation analysis highlighted that many genes linked to drug resistance and virulence in other pathogenicCandidaspecies are conserved inC. aurisand related species including expanded families of transporters and lipases, as well as mutations and copy number variants inERG11that confer drug resistance. In addition, we found genetic features of the emerging species that likely underlie differences in virulence and drug response between these and otherCandidaspecies, including genes involved in cell wall structure. To begin to characterize the species-specific genes important for antifungal response, we profiled the gene expression ofC. aurisin response to voriconazole and amphotericin B and found induction of several transporters and metabolic regulators that may play a role in drug resistance. This study provides a comprehensive view of the genomic basis of drug resistance, potential for mating, and virulence in this emerging fungal clade.
Abstract.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (In Press). Transcriptional heterogeneity ofCryptococcus gattiiVGII compared with non-VGII lineages underpins key pathogenicity pathways.
Abstract:
Transcriptional heterogeneity ofCryptococcus gattiiVGII compared with non-VGII lineages underpins key pathogenicity pathways
AbstractCryptococcus gattiiis a pathogenic yeast of humans and other animals, which causes disease predominantly in immunocompetent hosts. Infection begins when aerosolized yeast or spores enter the body, triggering an immune response, including engulfment by macrophages. To understand the early transcriptional signals in both the yeast and its mammalian host, we performed a time-course dual RNA-seq experiment for four lineages ofC. gattii(VGI-IV) interacting with mouse macrophages at 1hr, 3hr and 6hr post infection. Comparison ofin vitrotoex vivogene expression indicates lineage VGII is transcriptionally divergent to non-VGII lineages, including differential expression of genes involved in capsule synthesis, capsule attachment and ergosterol production. Various paralogs demonstrate sub-functionalisation between lineages including an upregulation of capsule biosynthesis-related geneCAP2, and downregulation ofCAP1in VGIII. Isolates also compensate for lineage-specific gene-losses by over-expression of genetically similar paralogs, including an over-expression of capsule geneCAS3in VGIV having lostCAS31. Differential expression of one in fiveC. gattiigenes was detected following co-incubation with mouse macrophages; all isolates showed high induction of oxidative-reduction functions and a downregulation of capsule attachment genes. We also show that VGII switches expression of two laccase paralogs (fromLAC1toLAC2) during co-incubation of macrophages. Finally, we found that mouse macrophages respond to all four lineages ofC. gattiiby upregulating FosB/Jun/Egr1 regulatory proteins at early time points. This study highlights the evolutionary breadth of expression profiles amongst the lineages ofC. gattiiand the diversity of transcriptional responses at this host-pathogen interface.ImportanceThe transcriptional profiles of related pathogens and their response to host induced stresses underpin their pathogenicity. Expression differences between related pathogens during host interaction can indicate when and how these genes contribute to virulence, ultimately informing new and improved treatment strategies for those diseases. In this paper, we compare the transcriptional profiles of five isolates representing four lineages ofC. gattiiin rich media. Our analyses identified key processes including cell capsule, ergosterol production and melanin that are differentially expressed between lineages, and we find that VGII has the most distinct profile in terms of numbers of differentially expressed genes. All lineages have also undergone sub-functionalisation for various paralogs including capsule biosynthesis and attachment genes. Most genes appeared down-regulated during co-incubation with macrophages, with the largest decrease observed for capsule attachment genes, which appears coordinated with a stress response, as all lineages also upregulated oxidative stress response genes. Furthermore, VGII upregulated many genes that are linked to ergosterol biosynthesis and switched expression of the laccaseLAC1toLAC2 ex vivo. Finally, we saw a pronounced increase in the FosB/Jun/Egr1 regulatory proteins at early time points in bone marrow derived macrophages, marking a role in the host response toC. gattii. This work highlights the dynamic roles of keyC. gattiivirulence genes in response to macrophages.
Abstract.
2020
Chybowska AD, Childers DS, Farrer RA (2020). Nine Things Genomics can Tell Us About Candida auris.
Frontiers in Genetics,
11Abstract:
Nine Things Genomics can Tell Us About Candida auris
© Copyright © 2020 Chybowska, Childers and Farrer. Candida auris is a recently emerged multidrug-resistant fungal pathogen causing severe illness in hospitalized patients. C. auris is most closely related to a few environmental or rarely observed but cosmopolitan Candida species. However, C. auris is unique in the concern it is generating among public health agencies for its rapid emergence, difficulty to treat, and the likelihood for further and more extensive outbreaks and spread. To date, five geographically distributed and genetically divergent lineages have been identified, none of which includes isolates that were collected prior to 1996. Indeed, C. auris’ ecological niche(s) and emergence remain enigmatic, although a number of hypotheses have been proposed. Recent genomic and transcriptomic work has also identified a variety of gene and chromosomal features that may have conferred C. auris with several important clinical phenotypes including its drug-resistance and growth at high temperatures. In this review we discuss nine major lines of enquiry into C. auris that big-data technologies and analytical approaches are beginning to answer.
Abstract.
Coelho C, Farrer RA (2020). Pathogen and host genetics underpinning cryptococcal disease. In (Ed)
Advances in Genetics, 1-66.
Abstract:
Pathogen and host genetics underpinning cryptococcal disease
Abstract.
2019
Farrer RA, Chang M, Davis MJ, van Dorp L, Yang D-H, Shea T, Sewell TR, Meyer W, Balloux F, Edwards HM, et al (2019). A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.
mBio,
10(6).
Abstract:
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands
ABSTRACT
We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa. All isolates were from environments (middens and tree holes) that are associated with a small mammal, the African hyrax. Phylogenetic and population genetic analyses confirmed that these isolates form a distinct, deeply divergent lineage, which we name VGV. VGV comprises two subclades (A and B) that are capable of causing mild lung infection with negligible neurotropism in mice. Comparing the VGV genome to previously identified lineages of C. gattii revealed a unique suite of genes together with gene loss and inversion events. However, standard URA5 restriction fragment length polymorphism (RFLP) analysis could not distinguish between VGV and VGIV isolates. We therefore developed a new URA5 RFLP method that can reliably identify the newly described lineage. Our work highlights how sampling understudied ecological regions alongside genomic and functional characterization can broaden our understanding of the evolution and ecology of major global pathogens.
IMPORTANCE Cryptococcus gattii is an environmental pathogen that causes severe systemic infection in immunocompetent individuals more often than in immunocompromised humans. Over the past 2 decades, researchers have shown that C. gattii falls within four genetically distinct major lineages. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drug-sensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (variety gattii five). The discovery of a new lineage from an understudied ecological region has far-reaching implications for the study and understanding of fungal pathogens and diseases they cause.
Abstract.
Full text.
Farrer RA (2019). Batrachochytrium salamandrivorans. Trends in Microbiology, 27(10), 892-893.
Ratti MF, Farrer RA, Cano LM, Faedda R, Goss EM (2019). Evaluation of High-Resolution Melting for Rapid Differentiation of Phytophthora Hybrids and Their Parental Species.
PLANT DISEASE,
103(9), 2295-2304.
Author URL.
Full text.
van Dorp L, Wang Q, Shaw LP, Acman M, Brynildsrud OB, Eldholm V, Wang R, Gao H, Yin Y, Chen H, et al (2019). Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains.
MICROBIAL GENOMICS,
5(4).
Author URL.
Full text.
2018
Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M, et al (2018). Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi.
SCIENTIFIC REPORTS,
8 Author URL.
Full text.
Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S (2018). Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.
EMERGING MICROBES & INFECTIONS,
7 Author URL.
Full text.
Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC, Schelenz S (2018). Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris (vol 7, pg 43, 2018).
EMERGING MICROBES & INFECTIONS,
7 Author URL.
Muñoz JF, Gade L, Chow NA, Loparev VN, Juieng P, Berkow EL, Farrer RA, Litvintseva AP, Cuomo CA (2018). Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.
Nat Commun,
9(1).
Abstract:
Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species.
Candida auris is an emergent multidrug-resistant fungal pathogen causing increasing reports of outbreaks. While distantly related to C. albicans and C. glabrata, C. auris is closely related to rarely observed and often multidrug-resistant species from the C. haemulonii clade. Here, we analyze near complete genome assemblies for the four C. auris clades and three related species, and map intra- and inter-species rearrangements across the seven chromosomes. Using RNA-Seq-guided gene predictions, we find that most mating and meiosis genes are conserved and that clades contain either the MTLa or MTLα mating loci. Comparing the genomes of these emerging species to those of other Candida species identifies genes linked to drug resistance and virulence, including expanded families of transporters and lipases, as well as mutations and copy number variants in ERG11. Gene expression analysis identifies transporters and metabolic regulators specific to C. auris and those conserved with related species which may contribute to differences in drug response in this emerging fungal clade.
Abstract.
Author URL.
Ene LV, Farrer RA, Hirakawa MP, Agwamba K, Cuomo CA, Bennett RJ (2018). Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,
115(37), E8688-E8697.
Author URL.
Full text.
Nash A, Sewell T, Farrer RA, Abdolrasouli A, Shelton JMG, Fisher MC, Rhodes J (2018). MARDy: Mycology Antifungal Resistance Database.
BIOINFORMATICS,
34(18), 3233-3234.
Author URL.
Full text.
O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M, et al (2018). Recent Asian origin of chytrid fungi causing global amphibian declines.
Science,
360(6389), 621-627.
Abstract:
Recent Asian origin of chytrid fungi causing global amphibian declines.
Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of the most devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.
Abstract.
Author URL.
Farrer RA, Ford CB, Rhodes J, Delorey T, May RC, Fisher MC, Cloutman-Green E, Balloux F, Cuomo CA (2018). Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways.
mSphere,
3(5).
Abstract:
Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways.
Cryptococcus gattii is a pathogenic yeast of humans and other animals which causes disease predominantly in immunocompetent hosts. Infection begins when aerosolized yeast or spores enter the body, triggering an immune response, including engulfment by macrophages. To understand the early transcriptional signals in both the yeast and its mammalian host, we performed a time-course dual-transcriptome sequencing (RNA-seq) experiment for four lineages of C. gattii (lineages VGI to IV) interacting with mouse macrophages at 1, 3, and 6 h postinfection. Comparisons of in vitro to ex vivo gene expression levels indicated that lineage VGII is transcriptionally divergent from non-VGII lineages, including differential expression of genes involved in capsule synthesis, capsule attachment, and ergosterol production. Several paralogous genes demonstrated subfunctionalization between lineages, including upregulation of capsule biosynthesis-related gene CAP2 and downregulation of CAP1 in VGIII. Isolates also compensate for lineage-specific gene losses by overexpression of genetically similar paralogs, including overexpression of capsule gene CAS3 in VGIV, which have lost the CAS31 gene. Differential expression of one in five C. gattii genes was detected following coincubation with mouse macrophages; all isolates showed high induction of oxidative-reduction functions and downregulation of capsule attachment genes. We also found that VGII switches expression of two laccase paralogs (from LAC1 to LAC2) during coincubation of macrophages. Finally, we found that mouse macrophages respond to all four lineages of C. gattii by upregulating FosB/Jun/Egr1 regulatory proteins at early time points. This report highlights the evolutionary breadth of expression profiles among the lineages of C. gattii and the diversity of transcriptional responses at this host-pathogen interface.IMPORTANCE the transcriptional profiles of related pathogens and their responses to host-induced stresses underpin their pathogenicity. Expression differences between related pathogens during host interaction can indicate when and how these genes contribute to virulence, ultimately informing new and improved treatment strategies for those diseases. In this paper, we compare the transcriptional profiles of five isolates representing four lineages of C. gattii in rich media. Our analyses identified key processes, including those involving cell capsule, ergosterol production, and melanin, that are differentially expressed between lineages, and we found that VGII has the most distinct profile in terms of numbers of differentially expressed genes. All lineages have also undergone subfunctionalization for several paralogs, including capsule biosynthesis and attachment genes. Most genes appeared downregulated during coincubation with macrophages, with the largest decrease observed for capsule attachment genes, which appeared to be coordinated with a stress response, as all lineages also upregulated oxidative stress response genes. Furthermore, VGII upregulated many genes that are linked to ergosterol biosynthesis and switched from expression of the laccase LAC1 to expression of LAC2 ex vivo Finally, we saw a pronounced increase in the FosB/Jun/Egr1 regulatory proteins at early time points in bone marrow-derived macrophages, marking a role in the host response to C. gattii This work highlights the dynamic roles of key C. gattii virulence genes in response to macrophages.
Abstract.
Author URL.
2017
Farrer R (2017). Candida auris gene annotations.
Abstract:
Candida auris gene annotations
A Hybrid assembly of Illumina and nanopore reads was performed for C. auris using SPAdes version 3.9.0, with default k-mer lengths and 1D scaffolding. Annotation was achieved using Genemark, BLASTx against Swissprot and KEGG, and HMMER hmmscan against PFAM and TIGRFAM. We also ran tRNAscan and Rnammer. to identify non-protein coding genes. Gene predictions were checked for a variety of issues including overlapping non-coding genes, overlaps coding genes, and containing in-frame stops. Genes were names according to BLAST and hmmer evidence in the following order of precedence: (1) Swissprot, (2) TIGRfam, and (3) KEGG, where BLAST hits must meet the 70% identity and 70% overlap criteria to be considered a good hit and for the name to be applied. Otherwise, genes are named hypothetical protein.
Abstract.
Farrer RA, Fisher MC (2017). Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. In (Ed)
FUNGAL PHYLOGENETICS AND PHYLOGENOMICS, 73-140.
Author URL.
Farrer RA, Martel A, Verbrugghe E, Abouelleil A, Ducatelle R, Longcore JE, James TY, Pasmans F, Fisher MC, Cuomo CA, et al (2017). Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.
Nat Commun,
8Abstract:
Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi.
To understand the evolutionary pathways that lead to emerging infections of vertebrates, here we explore the genomic innovations that allow free-living chytrid fungi to adapt to and colonize amphibian hosts. Sequencing and comparing the genomes of two pathogenic species of Batrachochytrium to those of close saprophytic relatives reveals that pathogenicity is associated with remarkable expansions of protease and cell wall gene families, while divergent infection strategies are linked to radiations of lineage-specific gene families. By comparing the host-pathogen response to infection for both pathogens, we illuminate the traits that underpin a strikingly different immune response within a shared host species. Our results show that, despite commonalities that promote infection, specific gene-family radiations contribute to distinct infection strategies. The breadth and evolutionary novelty of candidate virulence factors that we discover underscores the urgent need to halt the advance of pathogenic chytrids and prevent incipient loss of biodiversity.
Abstract.
Author URL.
Chen Y, Farrer RA, Giamberardino C, Sakthikumar S, Jones A, Yang T, Tenor JL, Wagih O, Van Wyk M, Govender NP, et al (2017). Microevolution of Serial Clinical Isolates of Cryptococcus neoformans var. grubii and C. gattii.
MBIO,
8(2).
Author URL.
Full text.
Farrer RA (2017). Synima: a Synteny imaging tool for annotated genome assemblies.
BMC Bioinformatics,
18(1).
Abstract:
Synima: a Synteny imaging tool for annotated genome assemblies.
BACKGROUND: Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes. RESULTS: Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima - and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License. CONCLUSIONS: Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.
Abstract.
Author URL.
Issi L, Farrer RA, Pastor K, Landry B, Delorey T, Bell GW, Thompson DA, Cuomo CA, Rao RP (2017). Zinc Cluster Transcription Factors Alter Virulence in Candida albicans.
GENETICS,
205(2), 559-576.
Author URL.
2016
Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M (2016). Comparative genomics of Fusarium oxysporum f. sp melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon.
NEW PHYTOLOGIST,
209(1), 307-318.
Author URL.
Muñoz JF, Farrer RA, Desjardins CA, Gallo JE, Sykes S, Sakthikumar S, Misas E, Whiston EA, Bagagli E, Soares CMA, et al (2016). Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.
mSphere,
1(5).
Abstract:
Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides.
The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp. we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.
Abstract.
Author URL.
Farrer R (2016). Homolaphlyctis polyrhiza Genome FASTA.
Abstract:
Homolaphlyctis polyrhiza Genome FASTA
Genome.fa
Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation CDS FASTA.
Abstract:
Homolaphlyctis polyrhiza annotation CDS FASTA
annotation.cds
Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation GFF3.
Abstract:
Homolaphlyctis polyrhiza annotation GFF3
annotation.gff3
Abstract.
Farrer R (2016). Homolaphlyctis polyrhiza annotation peptide FASTA.
Abstract:
Homolaphlyctis polyrhiza annotation peptide FASTA
annotation.pep
Abstract.
Leach MD, Farrer RA, Tan K, Miao Z, Walker LA, Cuomo CA, Wheeler RT, Brown AJP, Wong KH, Cowen LE, et al (2016). Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans.
Nature Communications,
7Abstract:
Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans
Fever is a universal response to infection, and opportunistic pathogens such as Candida albicans have evolved complex circuitry to sense and respond to heat. Here we harness RNA-seq and ChIP-seq to discover that the heat shock transcription factor, Hsf1, binds distinct motifs in nucleosome-depleted promoter regions to regulate heat shock genes and genes involved in virulence in C. albicans. Consequently, heat shock increases C. albicans host cell adhesion, damage and virulence. Hsf1 activation depends upon the molecular chaperone Hsp90 under basal and heat shock conditions, but the effects are opposite and in part controlled at the level of Hsf1 expression and DNA binding. Finally, we demonstrate that Hsp90 regulates global transcription programs by modulating nucleosome levels at promoters of stress-responsive genes. Thus, we describe a mechanism by which C. albicans responds to temperature via Hsf1 and Hsp90 to orchestrate gene expression and chromatin architecture, thereby enabling thermal adaptation and virulence.
Abstract.
Full text.
Farrer RA, Voelz K, Henk DA, Johnston SA, Fisher MC, May RC, Cuomo CA (2016). Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii.
Philos Trans R Soc Lond B Biol Sci,
371(1709).
Abstract:
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'.
Abstract.
Author URL.
2015
Farrer RA, Desjardins CA, Sakthikumar S, Gujja S, Saif S, Zeng Q, Chen Y, Voelz K, Heitman J, May RC, et al (2015). Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.
mBio,
6(5), e00868-e00815.
Abstract:
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii.
UNLABELLED: Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, and compared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. Through inclusion of population-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrial recombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur protein aconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positive selection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex. IMPORTANCE: the genetic differences between phenotypically different pathogens provide clues to the underlying mechanisms of those traits and can lead to new drug targets and improved treatments for those diseases. In this paper, we compare 16 genomes belonging to four highly differentiated lineages of Cryptococcus gattii, which cause pulmonary infections in otherwise healthy humans and other animals. Half of these lineages have not had their genomes previously assembled and annotated. We identified 15 ancestral rearrangements in the genome and over 700 genes that are unique to one or more lineages, many of which are associated with virulence. In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters. Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex.
Abstract.
Author URL.
2014
Martel A, Blooi M, Adriaensen C, Van Rooij P, Beukema W, Fisher MC, Farrer RA, Schmidt BR, Tobler U, Goka K, et al (2014). Recent introduction of a chytrid fungus endangers Western Palearctic salamanders.
SCIENCE,
346(6209), 630-631.
Author URL.
2013
Farrer RA, Henk DA, Garner TWJ, Balloux F, Woodhams DC, Fisher MC (2013). Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity.
PLOS GENETICS,
9(8).
Author URL.
Voelz K, Ma H, Phadke S, Byrnes EJ, Zhu P, Mueller O, Farrer RA, Henk DA, Lewit Y, Hsueh Y-P, et al (2013). Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii.
PLOS GENETICS,
9(9).
Author URL.
Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC (2013). Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Sci Rep,
3Abstract:
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate. We benchmark this method against other SNP callers using our FDR method with three fungal genomes, finding that it was able achieve a high level of accuracy. These tools are available at http://cfdr.sourceforge.net/.
Abstract.
Author URL.
Full text.
2012
Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al (2012). Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen.
PLOS PATHOGENS,
8(10).
Author URL.
2011
Farrer RA, Weinert LA, Bielby J, Garner TWJ, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, et al (2011). Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,
108(46), 18732-18736.
Author URL.
Fisher MC, Farrer RA (2011). Outbreaks and the emergence of novel fungal infections: Lessons from the panzootic of amphibian chytridiomycosis.
Journal of Invasive Fungal Infections,
5(3), 73-81.
Abstract:
Outbreaks and the emergence of novel fungal infections: Lessons from the panzootic of amphibian chytridiomycosis
Chytridiomycosis is a cutaneous infection of amphibians caused by the chytridiomycete fungal pathogen Batrachochytrium dendrobatidis (Bd). Despite being in a phylum not known for pathogenicity in vertebrates, Bd is now recognized as a primary driver of amphibian declines. Data show that this novel pathogen emerged in the 20th century to colonize amphibians worldwide. Such rapid emergence of a previously unrecognized pathogen illustrates many aspects of emerging fungal infections that threaten human health, namely long-distance human-mediated dispersal, multihost reservoirs, and altered virulence. In order to combat Bd, new tools have been developed to track its global spread and to analyze in parallel whole-genome diversity. This article details how such tools have applications to tracking and managing human fungal infections.
Abstract.
2010
Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RHY, Zody MC, Kunjeti SG, Donofrio NM, et al (2010). Genome evolution following host jumps in the Irish potato famine pathogen lineage.
Science,
330(6010), 1540-1543.
Abstract:
Genome evolution following host jumps in the Irish potato famine pathogen lineage.
Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.
Abstract.
Author URL.
2009
Farrer RA, Kemen E, Jones JDG, Studholme DJ (2009). De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.
FEMS Microbiol Lett,
291(1), 103-111.
Abstract:
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.
Illumina's Genome Analyzer generates ultra-short sequence reads, typically 36 nucleotides in length, and is primarily intended for resequencing. We tested the potential of this technology for de novo sequence assembly on the 6 Mbp genome of Pseudomonas syringae pv. syringae B728a with several freely available assembly software packages. Using an unpaired data set, velvet assembled >96% of the genome into contigs with an N50 length of 8289 nucleotides and an error rate of 0.33%. EDENA generated smaller contigs (N50 was 4192 nucleotides) and comparable error rates. SSAKE and VCAKE yielded shorter contigs with very high error rates. Assembly of paired-end sequence data carrying 400 bp inserts produced longer contigs (N50 up to 15 628 nucleotides), but with increased error rates (0.5%). Contig length and error rate were very sensitive to the choice of parameter values. Noncoding RNA genes were poorly resolved in de novo assemblies, while >90% of the protein-coding genes were assembled with 100% accuracy over their full length. This study demonstrates that, in practice, de novo assembly of 36-nucleotide reads can generate reasonably accurate assemblies from about 40 x deep sequence data sets. These draft assemblies are useful for exploring an organism's proteomic potential, at a very economic low cost.
Abstract.
Author URL.
Schornack S, Huitema E, Cano LM, Bozkurt TO, Oliva R, van Damme M, Schwizer S, Raffaele S, Chaparro-Garcia A, Farrer R, et al (2009). Ten things to know about oomycete effectors.
MOLECULAR PLANT PATHOLOGY,
10(6), 795-803.
Author URL.