Bioinformatics in Pathogenic Fungi

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 16595

Special Issue Editors


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Guest Editor
School of Medicine, University of California, San Diego, CA, USA
Interests: coccidioidomycosis; primary pathogenic fungi; pathogenesis; immunology

Special Issue Information

Dear Colleagues,

Many kinds of high-throughput experiments generate large data sets that require analysis by data science to produce summaries that can be further evaluated for potential biological significance. Some examples include genome sequencing, phylogenomics, genome-wide association studies, epigenetics, transcriptomics, proteomics, metabolomics and many others. This interface between biology and data science is known as bioinformatics and it has been a very active area of research recently. Optimal bioinformatic analysis requires an in-depth understanding of statistics and well as the development of a robust analytic pipeline. Bioinformatic techniques were initially used for the evaluation of fungal model organisms but have more recently been employed in all areas of biology, including the study of pathogenic fungi. This Special Issue focusses on bioinformatics in pathogenic fungi. Manuscripts concerning generation of data, data analysis, evaluation of different analytic methods and novel analytic methods for pathogenic fungi are all invited. Both research articles and review articles are welcome. Manuscripts submitted to the Journal of Fungi, which has an Impact Factor of 5.724, are reviewed promptly.

Dr. Theo N. Kirkland
Prof. Dr. Joshua Fierer
Guest Editors

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Keywords

  • pathogenic fungi
  • genomics
  • transcriptomics
  • proteomics
  • data science
  • computer science
  • bioinformatics

Published Papers (11 papers)

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Research

16 pages, 2385 KiB  
Article
Pins Gene Table v2.0: An Online Genome Database of 37 Pythium insidiosum Strains for Gene Content Exploration and Phylogenomic Analysis
by Weerayuth Kittichotirat, Preecha Patumcharoenpol, Thidarat Rujirawat, Sithichoke Tangphatsornruang, Chompoonek Yurayart and Theerapong Krajaejun
J. Fungi 2024, 10(2), 112; https://doi.org/10.3390/jof10020112 - 29 Jan 2024
Viewed by 901
Abstract
Unlike most pathogenic oomycetes, Pythium insidiosum infects humans and animals instead of plants. P. insidiosum has three clinically relevant genotypes/clades that cause a severe disease called pythiosis. To develop strategies for infection control, it is necessary to understand the biology and pathogenesis of [...] Read more.
Unlike most pathogenic oomycetes, Pythium insidiosum infects humans and animals instead of plants. P. insidiosum has three clinically relevant genotypes/clades that cause a severe disease called pythiosis. To develop strategies for infection control, it is necessary to understand the biology and pathogenesis of this pathogen. Investigating the evolutionary mechanisms behind the host-specific adaptation is vital, and comparative genomic analysis can help with this. To facilitate genomic analysis, an online bioinformatics tool called P. insidiosum (Pins) Gene Table v2.0 was developed. This tool includes genomic data from 37 genetically diverse P. insidiosum strains and four related species. The database contains 732,686 genes, grouped into 80,061 unique clusters and further divided into core and variable categories at genus, species, and genotype levels. A high-resolution phylogenomic relationship among P. insidiosum strains and other oomycetes was projected through hierarchical clustering and core gene analyses. 3156 P. insidiosum-specific genes were shared among all genotypes and may be responsible for causing disease in humans and animals. After comparing these species-specific genes to the MvirDB database, 112 had significant matches with 66 known virulence proteins, some of which might be involved in vascular occlusion, which is a pathological feature of pythiosis. The correlation of genotypes, geographic origins, and affected hosts of P. insidiosum suggests that clade-I strains are more specific to animals, while clade-II/III strains are more specific to humans. The clade-specific genes might link to host preference. In summary, Pins Gene Table v2.0 is a comprehensive genome database accessible to users with minimal bioinformatics experience for the analysis of P. insidiosum genomes. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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14 pages, 1565 KiB  
Article
Comparative Genomic Analysis of Colletotrichum lini Strains with Different Virulence on Flax
by Ekaterina M. Dvorianinova, Elizaveta A. Sigova, Timur D. Mollaev, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Roman O. Novakovskiy, Anastasia A. Turba, Daiana A. Zhernova, Elena V. Borkhert, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev
J. Fungi 2024, 10(1), 32; https://doi.org/10.3390/jof10010032 - 31 Dec 2023
Viewed by 1062
Abstract
Colletotrichum lini is a flax fungal pathogen. The genus comprises differently virulent strains, leading to significant yield losses. However, there were no attempts to investigate the molecular mechanisms of C. lini pathogenicity from high-quality genome assemblies until this study. In this work, we [...] Read more.
Colletotrichum lini is a flax fungal pathogen. The genus comprises differently virulent strains, leading to significant yield losses. However, there were no attempts to investigate the molecular mechanisms of C. lini pathogenicity from high-quality genome assemblies until this study. In this work, we sequenced the genomes of three C. lini strains of high (#390-1), medium (#757), and low (#771) virulence. We obtained more than 100× genome coverage with Oxford Nanopore Technologies reads (N50 = 12.1, 6.1, 5.0 kb) and more than 50× genome coverage with Illumina data (150 + 150 bp). Several assembly strategies were tested. The final assemblies were obtained using the Canu–Racon ×2–Medaka–Polca scheme. The assembled genomes had a size of 54.0–55.3 Mb, 26–32 contigs, N50 values > 5 Mb, and BUSCO completeness > 96%. A comparative genomic analysis showed high similarity among mitochondrial and nuclear genomes. However, a rearrangement event and the loss of a 0.7 Mb contig were revealed. After genome annotation with Funannotate, secreting proteins were selected using SignalP, and candidate effectors were predicted among them using EffectorP. The analysis of the InterPro annotations of predicted effectors revealed unique protein categories in each strain. The assembled genomes and the conducted comparative analysis extend the knowledge of the genetic diversity of C. lini and form the basis for establishing the molecular mechanisms of its pathogenicity. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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12 pages, 1536 KiB  
Article
Evaluation of Different Gene Prediction Tools in Coccidioides immitis
by Theo N. Kirkland, Sinem Beyhan and Jason E. Stajich
J. Fungi 2023, 9(11), 1094; https://doi.org/10.3390/jof9111094 - 09 Nov 2023
Viewed by 1020
Abstract
Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of the Coccidioides immitis RS genome (the reference strain of C. immitis) to annotations [...] Read more.
Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of the Coccidioides immitis RS genome (the reference strain of C. immitis) to annotations using the Funannotate and Augustus genome prediction pipelines. A total of 25% of the originally predicted genes (denoted CIMG) were not found in either the Funannotate or Augustus predictions. A comparison of Funannotate and Augustus predictions also found overlapping but not identical sets of genes. The predicted genes found only in the original annotation (referred to as CIMG-unique) were less likely to have a meaningful functional annotation and a lower number of orthologs and homologs in other fungi than all CIMG genes predicted by the original annotation. The CIMG-unique genes were also more likely to be lineage-specific and poorly expressed. In addition, the CIMG-unique genes were found in clusters and tended to be more frequently associated with transposable elements than all CIMG-predicted genes. The CIMG-unique genes were more likely to have experimentally determined transcription start sites that were further away from the originally predicted transcription start sites, and experimentally determined initial transcription was less likely to result in stable CIMG-unique transcripts. A sample of CIMG-unique genes that were relatively well expressed and differentially expressed in mycelia and spherules was inspected in a genome browser, and the structure of only about half of them was found to be supported by RNA-seq data. These data suggest that some of the CIMG-unique genes are not authentic gene predictions. Genes that were predicted only by the Funannotate pipeline were also less likely to have a meaningful functional annotation, be shorter, and express less well than all the genes predicted by Funannotate. C. immitis genes predicted by more than one annotation are more likely to have predicted functions, many orthologs and homologs, and be well expressed. Lineage-specific genes are relatively uncommon in this group. These data emphasize the importance and limitations of gene prediction software and suggest that improvements to the annotation of the C. immitis genome should be considered. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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13 pages, 1875 KiB  
Article
Genomic Sequence Resource of Talaromyces albobiverticillius, the Causative Pathogen of Pomegranate Pulp Rot Disease
by Tan Wang, Shuchang Chen, Qiuhong Niu, Guangling Xu, Chenxu Lu and Jin Zhang
J. Fungi 2023, 9(9), 909; https://doi.org/10.3390/jof9090909 - 07 Sep 2023
Viewed by 895
Abstract
Talaromyces albobiverticillius, a prominent pathogen responsible for pomegranate pulp rot disease, inflicts significant damage on Punica granatum L. Besides its pathogenicity, this fungus possesses the potential to produce substantial amounts of red pigments, making it promising for industrial applications. This study presents [...] Read more.
Talaromyces albobiverticillius, a prominent pathogen responsible for pomegranate pulp rot disease, inflicts significant damage on Punica granatum L. Besides its pathogenicity, this fungus possesses the potential to produce substantial amounts of red pigments, making it promising for industrial applications. This study presents the genome annotation of T. albobiverticillius field strain Tp-2, isolated from pomegranates. The genome assembly, generated through a combination of Oxford Nanopore and Illumina sequencing reads, yielded a high-quality assembly with 14 contigs, featuring an N50 length of 4,594,200 bp. The complete genome of strain Tp-2 spans 38,354,882 bp, with a GC content of 45.78%. Importantly, the assembly exhibits remarkable integrity, with 98.3% of complete Benchmarking Universal Single-Copy Orthologs validating genome completeness. Genome prediction analysis reveals the presence of 10,380 protein-coding genes. To our knowledge, this study is the first report on the genome sequence of T. albobiverticillius, offering valuable insights into its genetic variation and molecular mechanisms of pigment production. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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33 pages, 19965 KiB  
Article
Bioinformatic Analysis of Secondary Metabolite Biosynthetic Potential in Pathogenic Fusarium
by Chao Lin, Xi-long Feng, Yu Liu, Zhao-chen Li, Xiu-Zhang Li and Jianzhao Qi
J. Fungi 2023, 9(8), 850; https://doi.org/10.3390/jof9080850 - 15 Aug 2023
Cited by 1 | Viewed by 1455
Abstract
Fusarium species are among the filamentous fungi with the most pronounced impact on agricultural production and human health. The mycotoxins produced by pathogenic Fusarium not only attack various plants including crops, causing various plant diseases that lead to reduced yields and even death, [...] Read more.
Fusarium species are among the filamentous fungi with the most pronounced impact on agricultural production and human health. The mycotoxins produced by pathogenic Fusarium not only attack various plants including crops, causing various plant diseases that lead to reduced yields and even death, but also penetrate into the food chain of humans and animals to cause food poisoning and consequent health hazards. Although sporadic studies have revealed some of the biosynthetic pathways of Fusarium toxins, they are insufficient to satisfy the need for a comprehensive understanding of Fusarium toxin production. In this study, we focused on 35 serious pathogenic Fusarium species with available genomes and systematically analyzed the ubiquity of the distribution of identified Fusarium- and non-Fusarium-derived fungal toxin biosynthesis gene clusters (BGCs) in these species through the mining of core genes and the comparative analysis of corresponding BGCs. Additionally, novel sesterterpene synthases and PKS_NRPS clusters were discovered and analyzed. This work is the first to systematically analyze the distribution of related mycotoxin biosynthesis in pathogenic Fusarium species. These findings enhance the knowledge of mycotoxin production and provide a theoretical grounding for the prevention of fungal toxin production using biotechnological approaches. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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22 pages, 6666 KiB  
Article
Secretome Analysis for a New Strain of the Blackleg Fungus Plenodomus lingam Reveals Candidate Proteins for Effectors and Virulence Factors
by Nahla A. Bouqellah, Nadia A. Elkady and Peter F. Farag
J. Fungi 2023, 9(7), 740; https://doi.org/10.3390/jof9070740 - 11 Jul 2023
Cited by 1 | Viewed by 1388
Abstract
The fungal secretome is the main interface for interactions between the pathogen and its host. It includes the most important virulence factors and effector proteins. We integrated different bioinformatic approaches and used the newly drafted genome data of P. lingam isolate CAN1 (blackleg [...] Read more.
The fungal secretome is the main interface for interactions between the pathogen and its host. It includes the most important virulence factors and effector proteins. We integrated different bioinformatic approaches and used the newly drafted genome data of P. lingam isolate CAN1 (blackleg of rapeseed fungus) to predict the secretion of 217 proteins, including many cell-wall-degrading enzymes. All secretory proteins were identified; 85 were classified as CAZyme families and 25 were classified as protease families. Moreover, 49 putative effectors were predicted and identified, where 39 of them possessed at least one conserved domain. Some pectin-degrading enzymes were noticeable as a clustering group according to STRING web analysis. The secretome of P. lingam CAN1 was compared to the other two blackleg fungal species (P. lingam JN3 and P. biglobosus CA1) secretomes and their CAZymes and effectors were identified. Orthologue analysis found that P. lingam CAN1 shared 14 CAZy effectors with other related species. The Pathogen-Host Interaction database (PHI base) classified the effector proteins in several categories where most proteins were assigned as reduced virulence and two of them termed as hypervirulence. Nowadays, in silico approaches can solve many ambiguous issues about the mechanism of pathogenicity between fungi and plant host with well-designed bioinformatics tools. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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17 pages, 6503 KiB  
Article
Molecular Response of Meyerozyma guilliermondii to Patulin: Transcriptomic-Based Analysis
by Qiya Yang, Xi Zhang, Dhanasekaran Solairaj, Yu Fu and Hongyin Zhang
J. Fungi 2023, 9(5), 538; https://doi.org/10.3390/jof9050538 - 30 Apr 2023
Cited by 4 | Viewed by 1316
Abstract
Patulin (PAT), mainly produced by Penicillium expansum, is a potential threat to health. In recent years, PAT removal using antagonistic yeasts has become a hot research topic. Meyerozyma guilliermondii, isolated by our group, produced antagonistic effects against the postharvest diseases of [...] Read more.
Patulin (PAT), mainly produced by Penicillium expansum, is a potential threat to health. In recent years, PAT removal using antagonistic yeasts has become a hot research topic. Meyerozyma guilliermondii, isolated by our group, produced antagonistic effects against the postharvest diseases of pears and could degrade PAT in vivo or in vitro. However, the molecular responses of M. guilliermondii over PAT exposure and its detoxification enzymes are not apparent. In this study, transcriptomics is used to unveil the molecular responses of M. guilliermondii on PAT exposure and the enzymes involved in PAT degradation. The functional enrichment of differentially expressed genes indicated that the molecular response mainly includes the up-regulated expression of genes related to resistance and drug-resistance, intracellular transport, growth and reproduction, transcription, DNA damage repair, antioxidant stress to avoid cell damage, and PAT detoxification genes such as short-chain dehydrogenase/reductases. This study elucidates the possible molecular responses and PAT detoxification mechanism of M. guilliermondii, which could be helpful to further accelerate the commercial application of antagonistic yeast toward mycotoxin decontamination. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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13 pages, 2021 KiB  
Article
Hybrid De Novo Whole-Genome Assembly, Annotation, and Identification of Secondary Metabolite Gene Clusters in the Ex-Type Strain of Chrysosporium keratinophilum
by Alan Omar Granados-Casas, Angie Paola Sastoque, Alberto Miguel Stchigel, Ana Fernández-Bravo and José Francisco Cano-Lira
J. Fungi 2023, 9(4), 389; https://doi.org/10.3390/jof9040389 - 23 Mar 2023
Viewed by 1745
Abstract
Chrysosporium is a polyphyletic genus belonging (mostly) to different families of the order Onygenales (Eurotiomycetes, Ascomycota). Certain species, such as Chrysosporium keratinophilum, are pathogenic for animals, including humans, but are also a source of proteolytic enzymes (mainly keratinases) potentially useful in bioremediation. [...] Read more.
Chrysosporium is a polyphyletic genus belonging (mostly) to different families of the order Onygenales (Eurotiomycetes, Ascomycota). Certain species, such as Chrysosporium keratinophilum, are pathogenic for animals, including humans, but are also a source of proteolytic enzymes (mainly keratinases) potentially useful in bioremediation. However, only a few studies have been published regarding bioactive compounds, of which the production is mostly unpredictable due to the absence of high-quality genomic sequences. During the development of our study, the genome of the ex-type strain of Chrysosporium keratinophilum, CBS 104.66, was sequenced and assembled using a hybrid method. The results showed a high-quality genome of 25.4 Mbp in size spread across 25 contigs, with an N50 of 2.0 Mb, 34,824 coding sequences, 8002 protein sequences, 166 tRNAs, and 24 rRNAs. The functional annotation of the predicted proteins was performed using InterProScan, and the KEGG pathway mapping using BlastKOALA. The results identified a total of 3529 protein families and 856 superfamilies, which were classified into six levels and 23 KEGG categories. Subsequently, using DIAMOND, we identified 83 pathogen–host interactions (PHI) and 421 carbohydrate-active enzymes (CAZymes). Finally, the analysis using AntiSMASH showed that this strain has a total of 27 biosynthesis gene clusters (BGCs), suggesting that it has a great potential to produce a wide variety of secondary metabolites. This genomic information provides new knowledge that allows for a deeper understanding of the biology of C. keratinophilum, and offers valuable new information for further investigations of the Chrysosporium species and the order Onygenales. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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15 pages, 3182 KiB  
Article
A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates
by Luz Helena Patiño, Marina Muñoz, Angie Lorena Ramírez, Nórida Vélez, Patricia Escandón, Claudia-Marcela Parra-Giraldo and Juan David Ramírez
J. Fungi 2023, 9(2), 135; https://doi.org/10.3390/jof9020135 - 18 Jan 2023
Cited by 1 | Viewed by 1582
Abstract
Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic [...] Read more.
Cryptococcus neoformans species complexes are recognized as environmental fungi responsible for lethal meningoencephalitis in immunocompromised individuals. Despite the vast knowledge about the epidemiology and genetic diversity of this fungus in different regions of the world, more studies are necessary to comprehend the genomic profiles across South America, including Colombia, considered to be the second country with the highest number of Cryptococcosis. Here, we sequenced and analyzed the genomic architecture of 29 Colombian C. neoformans isolates and evaluated the phylogenetic relationship of these strains with publicly available C. neoformans genomes. The phylogenomic analysis showed that 97% of the isolates belonged to the VNI molecular type and the presence of sub-lineages and sub-clades. We evidenced a karyotype without changes, a low number of genes with copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs). Additionally, a difference in the number of SNPs between the sub-lineages/sub-clades was observed; some were involved in crucial fungi biological processes. Our study demonstrated the intraspecific divergence of C. neoformans in Colombia. These findings provide evidence that Colombian C. neoformans isolates do not probably require significant structural changes as adaptation mechanisms to the host. To the best of our knowledge, this is the first study to report the whole genome sequence of Colombian C. neoformans isolates. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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21 pages, 12068 KiB  
Article
The Botrytis cinerea Gene Expression Browser
by Gabriel Pérez-Lara, Tomás C. Moyano, Andrea Vega, Luis F. Larrondo, Rubén Polanco, José M. Álvarez, Daniel Aguayo and Paulo Canessa
J. Fungi 2023, 9(1), 84; https://doi.org/10.3390/jof9010084 - 06 Jan 2023
Viewed by 2341
Abstract
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application [...] Read more.
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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15 pages, 2219 KiB  
Article
Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii
by Claire A. Dubin, Mark Voorhies, Anita Sil, Marcus M. Teixeira, Bridget M. Barker and Rachel B. Brem
J. Fungi 2022, 8(12), 1235; https://doi.org/10.3390/jof8121235 - 22 Nov 2022
Viewed by 1239
Abstract
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious [...] Read more.
The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence–absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides. Full article
(This article belongs to the Special Issue Bioinformatics in Pathogenic Fungi)
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