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Jiang S, Chen Y, Han S, Lv L, Li L. Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 2022; 10:microorganisms10101882. [PMID: 36296159 PMCID: PMC9609632 DOI: 10.3390/microorganisms10101882] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) has become a widely used technology in biological research. NGS applications for clinical pathogen detection have become vital technologies. It is increasingly common to perform fast, accurate, and specific detection of clinical specimens using NGS. Pathogenic fungi with high virulence and drug resistance cause life-threatening clinical infections. NGS has had a significant biotechnological impact on detecting bacteria and viruses but is not equally applicable to fungi. There is a particularly urgent clinical need to use NGS to help identify fungi causing infections and prevent negative impacts. This review summarizes current research on NGS applications for fungi and offers a visual method of fungal detection. With the development of NGS and solutions for overcoming sequencing limitations, we suggest clinicians test specimens as soon as possible when encountering infections of unknown cause, suspected infections in vital organs, or rapidly progressive disease.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Shengyi Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou 310003, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, China
- Correspondence: ; Tel.: +86-0571-8723-6458
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Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJ, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CK, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ 2018; 6:e4392. [PMID: 29492338 PMCID: PMC5825881 DOI: 10.7717/peerj.4392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Inanc Birol
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Sandra Cervantes-Arango
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Braham Dhillon
- Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- FPInnovations, Vancouver, BC, Canada
| | - Padmini Herath
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Josyanne Lamarche
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Dario I. Ojeda
- Department of Biology Unit of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Monique L. Sakalidis
- Department of Plant, Soil & Microbial Sciences and Department of Forestry, Michigan State University, East Lansing, MI, United States of America
| | - Greg Taylor
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Clement K.M. Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Hesther Yueh
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
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Misas E, Muñoz JF, Gallo JE, McEwen JG, Clay OK. From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity. Comput Biol Chem 2016; 61:258-69. [PMID: 26970210 DOI: 10.1016/j.compbiolchem.2016.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 02/03/2016] [Accepted: 02/16/2016] [Indexed: 01/26/2023]
Abstract
The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention.
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Affiliation(s)
- Elizabeth Misas
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - José Fernando Muñoz
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia
| | - Juan Esteban Gallo
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan Guillermo McEwen
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Oliver Keatinge Clay
- Cellular & Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
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