1
|
Basenko EY, Shanmugasundram A, Böhme U, Starns D, Wilkinson PA, Davison HR, Crouch K, Maslen G, Harb OS, Amos B, McDowell MA, Kissinger JC, Roos DS, Jones A. What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics 2024; 227:iyae035. [PMID: 38529759 DOI: 10.1093/genetics/iyae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 03/27/2024] Open
Abstract
FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.
Collapse
Affiliation(s)
- Evelina Y Basenko
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Achchuthan Shanmugasundram
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
- Genomics England Limited, London E14 5AB, UK
| | - Ulrike Böhme
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - David Starns
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Paul A Wilkinson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Helen R Davison
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Kathryn Crouch
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Omar S Harb
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | - David S Roos
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| |
Collapse
|
2
|
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.
Collapse
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;
| |
Collapse
|
3
|
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.
Collapse
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:
| |
Collapse
|
4
|
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.
Collapse
|
5
|
de Melo Teixeira M, Stajich JE, Sahl JW, Thompson GR, Brem RB, Dubin CA, Blackmon AV, Mead HL, Keim P, Barker BM. A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain "Silveira". G3 (BETHESDA, MD.) 2022; 12:jkac031. [PMID: 35137016 PMCID: PMC8982387 DOI: 10.1093/g3journal/jkac031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022]
Abstract
Coccidioidomycosis is a common fungal disease that is endemic to arid and semi-arid regions of both American continents. Coccidioides immitis and Coccidioides posadasii are the etiological agents of the disease, also known as Valley Fever. For several decades, the C. posadasii strain Silveira has been used widely in vaccine studies, is the source strain for production of diagnostic antigens, and is a widely used experimental strain for functional studies. In 2009, the genome was sequenced using Sanger sequencing technology, and a draft assembly and annotation were made available. In this study, the genome of the Silveira strain was sequenced using single molecule real-time sequencing PacBio technology, assembled into chromosomal-level contigs, genotyped, and the genome was reannotated using sophisticated and curated in silico tools. This high-quality genome sequencing effort has improved our understanding of chromosomal structure, gene set annotation, and lays the groundwork for identification of structural variants (e.g. transversions, translocations, and copy number variants), assessment of gene gain and loss, and comparison of transposable elements in future phylogenetic and population genomics studies.
Collapse
Affiliation(s)
- Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília 70910-900, Brazil
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Claire A Dubin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Austin V Blackmon
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heather L Mead
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bridget M Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| |
Collapse
|
6
|
Duttke SH, Beyhan S, Singh R, Neal S, Viriyakosol S, Fierer J, Kirkland TN, Stajich JE, Benner C, Carlin AF. Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA. mSystems 2022; 7:e0140421. [PMID: 35076277 PMCID: PMC8788335 DOI: 10.1128/msystems.01404-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/04/2022] [Indexed: 01/07/2023] Open
Abstract
New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA. As RNA is nonpathogenic and can be readily isolated from inactivated infectious samples, csRNA-seq can detect acute changes in gene regulation within or in response to a pathogen with remarkable sensitivity under common laboratory conditions. Studying valley fever (coccidioidomycosis), an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health, we show how csRNA-seq can unravel transcriptional programs driving pathogenesis. Performing csRNA-seq on RNA isolated from different stages of the valley fever pathogen Coccidioides immitis revealed alternative promoter usage, connected cis-regulatory domains, and a WOPR family transcription factor, which are known regulators of virulence in other fungi, as being critical for pathogenic growth. We further demonstrate that a C. immitis WOPR homologue, CIMG_02671, activates transcription in a WOPR motif-dependent manner. Collectively, these findings provide novel insights into valley fever pathogenesis and provide a proof of principle for csRNA-seq as a powerful means to determine the genes, regulatory mechanisms, and transcription factors that control the pathogenesis of highly infectious agents. IMPORTANCE Infectious pathogens like airborne viruses or fungal spores are difficult to study; they require high-containment facilities, special equipment, and expertise. As such, establishing approaches such as genome editing or other means to identify the factors and mechanisms underlying caused diseases, and, thus, promising drug targets, is costly and time-intensive. These obstacles particularly hinder the analysis of new, emerging, or rare infectious diseases. We recently developed a method termed capped small RNA sequencing (csRNA-seq) that enables capturing acute changes in active gene expression from total RNA. Prior to csRNA-seq, such an analysis was possible only by using living cells or nuclei, in which pathogens are highly infectious. The process of RNA purification, however, inactivates pathogens and thus enables the analysis of gene expression during disease progression under standard laboratory conditions. As a proof of principle, here, we use csRNA-seq to unravel the gene regulatory programs and factors likely critical for the pathogenesis of valley fever, an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health.
Collapse
Affiliation(s)
- Sascha H. Duttke
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sinem Beyhan
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- J. Craig Venter Institute, Department of Infectious Diseases, La Jolla, California, USA
| | - Rajendra Singh
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Sonya Neal
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Suganya Viriyakosol
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| | - Joshua Fierer
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Infectious Diseases Section, VA Healthcare San Diego, San Diego, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Theo N. Kirkland
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
- Department of Pathology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, California, USA
| | - Christopher Benner
- Department of Medicine, Division of Endocrinology, UC San Diego School of Medicine, La Jolla, California, USA
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Disease, UC San Diego School of Medicine, La Jolla, California, USA
| |
Collapse
|
7
|
Mat Razali N, Hisham SN, Kumar IS, Shukla RN, Lee M, Abu Bakar MF, Nadarajah K. Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani. Int J Mol Sci 2021; 22:ijms22042183. [PMID: 33671736 PMCID: PMC7926851 DOI: 10.3390/ijms22042183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.
Collapse
Affiliation(s)
- Nurhani Mat Razali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Siti Norvahida Hisham
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Ilakiya Sharanee Kumar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Rohit Nandan Shukla
- Bionivid Technology Pte Ltd., 209, 4th Cross Rd, B Channasandra, East of NGEF Layout, Kasturi Nagar, Bengaluru 560043, Karnataka, India;
| | - Melvin Lee
- Codon Genomics Sdn. Bhd., No 26, Jalan Dutamas 7 Taman Dutamas Balakong, Seri Kembangan 43200, Selangor, Malaysia;
| | | | - Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
- Correspondence:
| |
Collapse
|
8
|
Malavia D, Gow NAR, Usher J. Advances in Molecular Tools and In Vivo Models for the Study of Human Fungal Pathogenesis. Microorganisms 2020; 8:E803. [PMID: 32466582 PMCID: PMC7356103 DOI: 10.3390/microorganisms8060803] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogenic fungi represent an increasing infectious disease threat to humans, especially with an increasing challenge of antifungal drug resistance. Over the decades, numerous tools have been developed to expedite the study of pathogenicity, initiation of disease, drug resistance and host-pathogen interactions. In this review, we highlight advances that have been made in the use of molecular tools using CRISPR technologies, RNA interference and transposon targeted mutagenesis. We also discuss the use of animal models in modelling disease of human fungal pathogens, focusing on zebrafish, the silkworm, Galleria mellonella and the murine model.
Collapse
Affiliation(s)
| | | | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK; (D.M.); (N.A.R.G.)
| |
Collapse
|
9
|
Teixeira MDM, Barker BM, Stajich JE. Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State. Microbiol Resour Announc 2019; 8:e00149-19. [PMID: 31416856 PMCID: PMC6696631 DOI: 10.1128/mra.00149-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/18/2019] [Indexed: 11/20/2022] Open
Abstract
Coccidioides fungi are widely distributed in the American continents, with an expanding western range documented by a recently discovered cryptic population of Coccidioides immitis in Washington State. The assembled and annotated reference genome sequence of the soil-derived C. immitis strain WA_211 will support population and functional genomics studies.
Collapse
Affiliation(s)
- Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília, Brasília, Federal District, Brazil
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bridget Marie Barker
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| |
Collapse
|
10
|
Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Transposable elements contribute to fungal genes and impact fungal lifestyle. Sci Rep 2019; 9:4307. [PMID: 30867521 PMCID: PMC6416283 DOI: 10.1038/s41598-019-40965-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
The last decade brought a still growing experimental evidence of mobilome impact on host's gene expression. We systematically analysed genomic location of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in order to explore their potential roles in genome evolution and correlation with species' lifestyle. We found that non-autonomous TEs and remnant copies are evenly distributed across genomes. In consequence, they also massively overlap with regions annotated as genes, which suggests a great contribution of TE-derived sequences to host's coding genome. Younger and potentially active TEs cluster with one another away from genic regions. This non-randomness is a sign of either selection against insertion of TEs in gene proximity or target site preference among some types of TEs. Proteins encoded by genes with old transposable elements insertions have significantly less repeat and protein-protein interaction motifs but are richer in enzymatic domains. However, genes only proximal to TEs do not display any functional enrichment. Our findings show that adaptive cases of TE insertion remain a marginal phenomenon, and the overwhelming majority of TEs are evolving neutrally. Eventually, animal-related and pathogenic fungi have more TEs inserted into genes than fungi with other lifestyles. This is the first systematic, kingdom-wide study concerning mobile elements and their genomic neighbourhood. The obtained results should inspire further research concerning the roles TEs played in evolution and how they shape the life we know today.
Collapse
Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| |
Collapse
|
11
|
Kirkland TN. Special Issue: Genomic Data in Pathogenic Fungi. J Fungi (Basel) 2018; 4:jof4010040. [PMID: 29558447 PMCID: PMC5872343 DOI: 10.3390/jof4010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 11/16/2022] Open
Abstract
This special issue, "Genomic Data in Pathogenic Fungi," focuses on the genomics of human and plant pathogens. Efforts like this are important because so little information about these organisms is available.[...].
Collapse
Affiliation(s)
- Theo N Kirkland
- Departments of Pathology and Medicine, School of Medicine, University of California, San Diego, CA 92037, USA.
| |
Collapse
|
12
|
Kirkland TN, Fierer J. Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity. Virulence 2018; 9:1426-1435. [PMID: 30179067 PMCID: PMC6141143 DOI: 10.1080/21505594.2018.1509667] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/31/2018] [Indexed: 11/24/2022] Open
Abstract
Coccidioides immitis and C. posadasii are two highly pathogenic dimorphic fungal species that are endemic in the arid areas of the new world, including the region from west Texas to southern and central California in the USA that cause coccidioidomycosis (also known as Valley Fever). In highly endemic regions such as southern Arizona, up to 50% of long term residents have been infected. New information about fungal population genetics, ecology, epidemiology, and host-pathogen interactions is becoming available. However, our understanding of some aspects of coccidioidomycosis is still incomplete, including the extent of genetic variability of the fungus, the genes involved in virulence, and how the changes in gene expression during the organism's dimorphic life cycle are related to the transformation from a free-living mold to a parasitic spherule. Unfortunately, efforts to develop an effective subunit vaccine have not yet been productive, although two potential live fungus vaccines have been developed.
Collapse
Affiliation(s)
- Theo N. Kirkland
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Joshua Fierer
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, San Diego, CA, USA
- VA Healthcare San Diego, San Diego, CA, USA
| |
Collapse
|