A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex
United States Department of Agriculture1, Centraalbureau voor Schimmelcultures2, Landcare Research3, Louisiana State University4, Wageningen University and Research Centre5, International Sleep Products Association6, Pennsylvania State University7, Dutch Ministry of Agriculture, Nature and Food Quality8, New Zealand Institute for Crop and Food Research9, University of Texas Health Science Center at San Antonio10, Technical University of Denmark11, University of Florida12, University of California, Davis13, University of Idaho14
TL;DR: Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant, and revealed that the 26 STs associated with human mycoses were genetically diverse, including several which appear to be nosocomial in origin.
About: This article is published in Fungal Genetics and Biology.The article was published on 2009-12-01. It has received 306 citations till now. The article focuses on the topics: Ribosomal DNA & Intergenic region.
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TL;DR: A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades, and the taxonomic placement of the genus is discussed.
686 citations
Cites methods from "A two-locus DNA sequence database f..."
...…used for diagnostic purposes in the Fungi, especially beta-tubulin (TUB2) and calmodulin (e.g. for Aspergillus and Penicillium; Samson et al. 2007, Peterson 2008, Houbraken et al. 2011), TEF1 (for Fusarium; Geiser et al. 2004, O’Donnell et al. 2009) and COX1 (for Penicillium; Seifert et al. 2007)....
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United States Department of Agriculture1, University of Texas Health Science Center at San Antonio2, University of Idaho3, Centers for Disease Control and Prevention4, Centraalbureau voor Schimmelcultures5, Rutgers University6, University of Tsukuba7, Seoul National University8, Pennsylvania State University9
TL;DR: A three-locus DNA sequence database is constructed to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories.
Abstract: Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1 (EF-1), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate’s clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.
385 citations
TL;DR: An overview of the Panama disease and its causal agent, Fusarium oxysporum f. cubense, is presented in this paper, with an emphasis on tropical race 4 (TR4), a 'Cavendish'-killing variant of the pathogen that has spread dramatically in the Eastern Hemisphere.
Abstract: Banana (Musa spp.) is one of the world's most important fruits. In 2011, 145 million metric tons, worth an estimated $44 billion, were produced in over 130 countries. Fusarium wilt (also known as Panama disease) is one of the most destructive diseases of this crop. It devastated the 'Gros Michel'-based export trades before the mid-1900s, and threatens the Cavendish cultivars that were used to replace it; in total, the latter cultivars are now responsible for approximately 45% of all production. An overview of the disease and its causal agent, Fusarium oxysporum f. sp. cubense, is presented below. Despite a substantial positive literature on biological, chemical, or cultural measures, management is largely restricted to excluding F. oxysporum f. sp. cubense from noninfested areas and using resistant cultivars where the pathogen has established. Resistance to Fusarium wilt is poor in several breeding targets, including important dessert and cooking cultivars. Better resistance to this and other diseases is needed. The history and impact of Fusarium wilt is summarized with an emphasis on tropical race 4 (TR4), a 'Cavendish'-killing variant of the pathogen that has spread dramatically in the Eastern Hemisphere.
362 citations
Journal Article•
TL;DR: This paper proposed a polyphasic approach to the recognition and identification of species within Colletotrichum, matching genetic distinctness with informative morphological and biological characters, including morphology, pathogenicity, physiology, phylogenetics and secondary metabolite production.
Abstract: Colletotrichum is the causal agent of anthracnose and other diseases on leaves, stems and fruits of numerous plant species, including several important crops. Accurate species identification is critical to understand the epidemiology and to develop effective control of these diseases. Morphologically-based identification of Colletotrichum species has always been problematic, because there are few reliable characters and many of these characters are plastic, dependent upon methods and experimental conditions. Rapid progress in molecular phylogenetic methods is now making it possible to recognise stable and well-resolved clades within Colletotrichum. How these should be reflected in a classification system remains to be resolved. An important step in providing a stable taxonomy for the genus is to epitypify existing names, and in so doing link them to genetically defined clades. We recommend a polyphasic approach to the recognition and identification of species within Colletotrichum, matching genetic distinctness with informative morphological and biological characters. This paper reviews various approaches in the study of Colletotrichum complexes including morphology, pathogenicity, physiology, phylogenetics and secondary metabolite production. A backbone phylogenetic tree using ITS sequence data from 42 ex-type specimens has been generated. Phylogenetic analysis using ITS sequence data is a useful tool to give a preliminarily identification for Colletotrichum species or place them in species complexes. However, caution must be taken here as the majority of the ITS sequences deposited in GenBank are wrongly named. Multi-gene phylogenetic data provides much better understanding of the relationships within Colletotrichum and should be employed where possible. We propose that an ideal approach for Colletotrichum systematics should be based on a multi-gene phylogeny, with comparison made with type specimens, and a well-defined phylogenetic lineage should be in conjunction with recognisable polyphasic characters, such as morphology, physiology, pathogenicity, cultural characteristics and secondary metabolites. Finally a set of protocols and methodologies is provided as a guideline for future studies, epitypification and the description of new species.
357 citations
TL;DR: The analyses revealed that Cylindrocarpon formed a basal monophyletic sister to a 'terminal Fusarium clade' (TFC) comprising 20 strongly supported species complexes and nine monotypic lineages, which the authors provisionally recognize as Fusaria.
325 citations
Cites background from "A two-locus DNA sequence database f..."
...Although the oxysporum species complex collectively comprises the largest group of phytopathogenic fusaria (O’Donnell et al., 2009), they represent a surprisingly recent radiation dated to the late Pliocene 1....
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References
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15 Jan 2001
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Abstract: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefeller University, Texas Tech, Cold Spring Harbor Laboratory, Washington University, and other leading institutions. The theoretical and historical underpinnings of techniques are prominent features of the presentation throughout, information that does much to help trouble-shoot experimental problems. For the fourth edition of this classic work, the content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories. Core chapters from the third edition have been revised to feature current strategies and approaches to the preparation and cloning of nucleic acids, gene transfer, and expression analysis. They are augmented by 12 new chapters which show how DNA, RNA, and proteins should be prepared, evaluated, and manipulated, and how data generation and analysis can be handled. The new content includes methods for studying interactions between cellular components, such as microarrays, next-generation sequencing technologies, RNA interference, and epigenetic analysis using DNA methylation techniques and chromatin immunoprecipitation. To make sense of the wealth of data produced by these techniques, a bioinformatics chapter describes the use of analytical tools for comparing sequences of genes and proteins and identifying common expression patterns among sets of genes. Building on thirty years of trust, reliability, and authority, the fourth edition of Mol
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TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Abstract: Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Contact: clustalw@ucd.ie
25,325 citations
TL;DR: The present version of DnaSP introduces several new modules and features which, among other options, allow handling big data sets and conducting a large number of coalescent-based tests by Monte Carlo computer simulations.
Abstract: Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
6,100 citations
"A two-locus DNA sequence database f..." refers methods in this paper
...Approximately 5 lg of restricted genomic DNA was loaded into each lane and DNA was blotted onto nitrocellulose membranes and probed using standard methods (Sambrook et al., 1989)....
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3,857 citations
"A two-locus DNA sequence database f..." refers methods in this paper
...Compatibility between the EF-1a and IGS rDNA datasets was assessed using the partition-homogeneity test (PHT; Farris et al., 1994) as implemented in PAUP*, and Compat.py version 3.0 (Kauff and Lutzoni, 2002a,b)....
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Dissertation•
01 Jan 2006
TL;DR: A fast and accurate algorithm that allows ML phylogenetic searches to be performed on datasets consisting of thousands of sequences and the P-GARLI algorithm extends the approach of GARLI to allow simultaneous use of many computer processors.
Abstract: Phylogenetic trees have a multitude of applications in biology, epidemiology, conservation and even forensics. However, the inference of phylogenetic trees can be extremely computationally intensive. The computational burden of such analyses becomes even greater when model-based methods are used. Model-based methods have been repeatedly shown to be the most accurate choice for the reconstruction of phylogenetic trees, and thus are an attractive choice despite their high computational demands. Using the Maximum Likelihood (ML) criterion to choose among phylogenetic trees is one commonly used model-based technique. Until recently, software for performing ML analyses of biological sequence data was largely intractable for more vi than about one hundred sequences. Because advances in sequencing technology now make the assembly of datasets consisting of thousands of sequences common, ML search algorithms that are able to quickly and accurately analyze such data must be developed if ML techniques are to remain a viable option in the future. I have developed a fast and accurate algorithm that allows ML phylogenetic searches to be performed on datasets consisting of thousands of sequences. My software uses a genetic algorithm approach, and is named GARLI (Genetic Algorithm for Rapid Likelihood Inference). The speed of this new algorithm results primarily from its novel technique for partial optimization of branch-length parameters following topological rearrangements. Experiments performed with GARLI show that it is able to analyze large datasets in a small fraction of the time required by the previous generation of search algorithms. The program also performs well relative to two other recently introduced fast ML search programs. Large parallel computer clusters have become common at academic institutions in recent years, presenting a new resource to be used for phylogenetic analyses. The P-GARLI algorithm extends the approach of GARLI to allow simultaneous use of many computer processors. The processors may be instructed to work together on a phylogenetic search in either a highly coordinated or largely independent fashion.
3,391 citations
"A two-locus DNA sequence database f..." refers methods in this paper
...The collapsed 256 isolate dataset, which contained all of the unique two-locus haplotypes, was used for all subsequent phylogenetic analyses employing maximum parsimony (MP; Swofford, 2002) and maximum likelihood (ML; Zwickl, 2006)....
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...The best ML tree received a negative log likelihood ( ln L) score of 18318.888549 based on the results of ten independent ML heuristic phylogenetic analyses, using the GTR + I + C model of nucleotide substitution in GARLI version 0.96 (Zwickl, 2006)....
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