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Kirkland TN, Beyhan S, Stajich JE. Evaluation of Different Gene Prediction Tools in Coccidioides immitis. J Fungi (Basel) 2023; 9:1094. [PMID: 37998899 PMCID: PMC10672684 DOI: 10.3390/jof9111094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
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 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.
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Affiliation(s)
- Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, School of Medicine, University of California, La Jolla, CA 92093, USA;
- Department of Pathology, School of Medicine, University of California, La Jolla, CA 92093, USA
| | - Sinem Beyhan
- Department of Medicine, Division of Infectious Disease, School of Medicine, University of California, La Jolla, CA 92093, USA;
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92521, USA;
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Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB. Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8121235. [PMID: 36547568 PMCID: PMC9782707 DOI: 10.3390/jof8121235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
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 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.
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Affiliation(s)
- Claire A. Dubin
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Department of Microbiology and Immunology, UC San Francisco, San Francisco, CA 94143, USA
| | - Marcus M. Teixeira
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília 70910-900, Brazil
| | - Bridget M. Barker
- The Translational Genomics Research Institute (TGen)-Affiliate of City of Hope, Flagstaff, AZ 85004, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Rachel B. Brem
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720-3102, USA
- Correspondence:
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Cai H, Zhang H, Guo DH, Wang Y, Gu J. Genomic Data Mining Reveals Abundant Uncharacterized Transporters in Coccidioides immitis and Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8101064. [PMID: 36294626 PMCID: PMC9604845 DOI: 10.3390/jof8101064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/01/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better understanding of Coccidioides biology and new antifungal strategies. Transporters play essential roles in pathogen survival, growth, infection, and adaptation, and are considered as potential drug targets. However, the composition and roles of transport machinery in Coccidioides remain largely unknown. In this study, genomic data mining revealed an abundant, uncharacterized repertoire of transporters in Coccidioides genomes. The catalog included 1288 and 1235 transporter homologs in C. immitis and C. posadasii, respectively. They were further annotated to class, subclass, family, subfamily and range of substrates based on the Transport Classification (TC) system. They may play diverse roles in nutrient uptake, metabolite secretion, ion homeostasis, drug efflux, or signaling. This study represents an initial effort for a systems-level characterization of the transport machinery in these understudied fungal pathogens.
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Affiliation(s)
- Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Daniel H. Guo
- Strake Jesuit College Preparatory, Houston, TX 77036, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Correspondence: (Y.W.); (J.G.)
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Correspondence: (Y.W.); (J.G.)
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Coccidioidomycosis in Northern Arizona: an Investigation of the Host, Pathogen, and Environment Using a Disease Triangle Approach. mSphere 2022; 7:e0035222. [PMID: 35972134 PMCID: PMC9599602 DOI: 10.1128/msphere.00352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are the etiological agents of coccidioidomycosis (Valley fever [VF]). Disease manifestation ranges from mild pneumonia to chronic or extrapulmonary infection. If diagnosis is delayed, the risk of severe disease increases. In this report, we investigated the intersection of pathogen, host, and environment for VF cases in Northern Arizona (NAZ), where the risk of acquiring the disease is much lower than in Southern Arizona. We investigated reported cases and assessed pathogen origin by comparing genomes of NAZ clinical isolates to isolates from other regions. Lastly, we surveyed regional soils for presence of Coccidioides. We found that cases of VF increased in NAZ in 2019, and Coccidioides NAZ isolates are assigned to Arizona populations using phylogenetic inference. Importantly, we detected Coccidioides DNA in NAZ soil. Given recent climate modeling of the disease that predicts that cases will continue to increase throughout the region, and the evidence presented in this report, we propose that disease awareness outreach to clinicians throughout the western United States is crucial for improving patient outcomes, and further environmental sampling across the western U.S. is warranted. IMPORTANCE Our work is the first description of the Valley fever disease triangle in Northern Arizona, which addresses the host, the pathogen, and the environmental source in the region. Our data suggest that the prevalence of diagnosed cases rose in 2019 in this region, and some severe cases necessitate hospitalization. We present the first evidence of Coccidioides spp. in Northern Arizona soils, suggesting that the pathogen is maintained in the local environment. Until disease prevention is an achievable option via vaccination, we predict that incidence of Valley fever will rise in the area. Therefore, enhanced awareness of and surveillance for coccidioidomycosis is vital to community health in Northern Arizona.
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Coccidioides Species: A Review of Basic Research: 2022. J Fungi (Basel) 2022; 8:jof8080859. [PMID: 36012847 PMCID: PMC9409882 DOI: 10.3390/jof8080859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Coccidioides immitis and posadasii are closely related fungal species that cause coccidioidomycosis. These dimorphic organisms cause disease in immunocompetent as well as immunocompromised individuals and as much as 40% of the population is infected in the endemic area. Although most infections resolve spontaneously, the infection can be prolonged and, in some instances, fatal. Coccidioides has been studied for more than 100 years and many aspects of the organism and the disease it causes have been investigated. There are over 500 manuscripts concerning Coccidioides (excluding clinical articles) referenced in PubMed over the past 50 years, so there is a large body of evidence to review. We reviewed the most accurate and informative basic research studies of these fungi including some seminal older studies as well as an extensive review of current research. This is an attempt to gather the most important basic research studies about this fungus into one publication. To focus this review, we will discuss the mycology of the organism exclusively rather than the studies of the host response or clinical studies. We hope that this review will be a useful resource to those interested in Coccidioides and coccidioidomycosis.
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Abstract
AbstractThe order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.
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Gorris ME, Caballero Van Dyke MC, Carey A, Hamm PS, Mead HL, Uehling JK. A Review of Coccidioides Research, Outstanding Questions in the Field, and Contributions by Women Scientists. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021; 8:114-128. [PMID: 34367880 PMCID: PMC8327307 DOI: 10.1007/s40588-021-00173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 12/19/2022]
Abstract
Purpose of Review Coccidioidomycosis is an infectious disease that gained clinical significance in the early 20th century. Many of the foundational contributions to coccidioidomycosis research, including the discovery of the fungal disease agent, Coccidioides spp., were made by women. We review recent progress in Coccidioides research and big questions remaining in the field, while highlighting some of the contributions from women. Recent Findings New molecular-based techniques provide a promising method for detecting Coccidioides, which can help determine the dominate reservoir host and ideal environmental conditions for growth. Genetic and genomic analyses have allowed an understanding of population structure, species level diversity, and evolutionary histories. We present a current, comprehensive genome list, where women contributed many of these entries. Several efforts to develop a coccidioidomycosis vaccine are underway. Summary Women continue to pioneer research on Coccidioides, including the relationships between the fungi and the environment, genetics, and clinical observations. Significant questions remain in the field of Coccidioides, including the main host reservoir, the relationships between genotypic and phenotypic variation, and the underlying cause for chronic clinical coccidioidomycosis cases.
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Affiliation(s)
- Morgan E Gorris
- Los Alamos National Laboratory, Information Systems and Modeling & Center for Nonlinear Studies, Los Alamos, NM USA
| | | | - Adrienne Carey
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Paris S Hamm
- Department of Biology, University of New Mexico, Albuquerque, NM USA
| | - Heather L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ USA
| | - Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR USA
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de Melo Teixeira M, Lang BF, Matute DR, Stajich JE, Barker BM. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 (BETHESDA, MD.) 2021; 11:jkab132. [PMID: 33871031 PMCID: PMC8496281 DOI: 10.1093/g3journal/jkab132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.
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Affiliation(s)
- Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Faculty of Medicine, University of Brasília-DF, Brasília, Federal District 70910-3300, Brazil
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Génomiques, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Powell D, Jones A, Jackson N, Kaur P, Bar I, Schwessinger B, Frère CH. Genome Sequence of the Fungus Nannizziopsis barbatae, an Emerging Reptile Pathogen. Microbiol Resour Announc 2021; 10:e01213-20. [PMID: 33414335 PMCID: PMC8407711 DOI: 10.1128/mra.01213-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 12/04/2022] Open
Abstract
Nannizziopsis barbatae is an emerging fungal pathogen capable of causing contagious dermatomycosis in reptiles. Here, we report a 31.54-Mb draft genome sequence of an isolate originating from an infected eastern water dragon in Brisbane, Australia.
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Affiliation(s)
- Daniel Powell
- Global Change Ecology Research Group, School of Science, Technology, and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Ashley Jones
- Research School of Biology, The Australian National University, Acton, Canberra, ACT, Australia
| | - Nicola Jackson
- Global Change Ecology Research Group, School of Science, Technology, and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, Faculty of Science, University of Western Australia, Perth, WA, Australia
| | - Ido Bar
- Environmental Futures Research Institute, School of Environment and Sciences, Griffith University, Nathan, QLD, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, ACT, Australia
| | - Céline H Frère
- Global Change Ecology Research Group, School of Science, Technology, and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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