Printer Friendly
The Free Library
22,725,466 articles and books

Comparison of general fungal and basidiomycete-specific ITS primers for identification of wood decay fungi.



Abstract

The identity of the fungi associated with and responsible for wood decay could lead to the development of more environmentally benign wood preservative systems. In this study we have reconstructed the phylogenetic tree of a select group of basidiomycete basidiomycete

Any of a large and diverse class of fungi (division Mycota), including jelly and shelf, or bracket, fungi; mushrooms, puffballs, and stinkhorns; and the rusts and smuts.
 fungi using nucleotide sequences of the internal transcribed spacer ITS (for internal transcribed spacer) refers to a piece of non-functional RNA situated between structural ribosomal RNAs (rRNA) on a common precursor transcript. Read from 5' to 3', this polycistronic rRNA precursor transcript contains the 5' external transcribed sequence (5' ETS),  (ITS) region. We then compared this to trees generated from restriction fragment length polymorphism restriction fragment length polymorphism
n. Abbr. RFLP
Intraspecies variations in the length of DNA fragments generated by the action of restriction enzymes and caused by mutations that alter the sites at which these enzymes act, changing
 (RFLP RFLP
abbr.
restriction fragment length polymorphism



RFLP

restriction fragment length polymorphism.

RFLP 
) analysis using two different primers to see if the latter procedures can correctly identify multiple isolates of select wood decay fungi. The phylogenetic tree using maximum likelihood analysis revealed three well-supported genera, Trametes, Phanerochaete, and Gloeophyllum, with bootstrap values of 75 or greater. Trametes and Phanerochaete were sister taxa, and Gloeophyllum was a sister taxon taxon (pl. taxa), in biology, a term used to denote any group or rank in the classification of organisms, e.g., class, order, family.  to the Trametes/Phanerochaete clade clade Cladus, subtype Genetics A branch of biological taxa or species that share features inherited from a common ancestor; a single phylogenetic group or line. See Inheritance, Species. . Neither set of RFLP data could resolve the three genera into monophyletic monophyletic /mono·phy·let·ic/ (mon?o-fi-let´ik) descended from a common ancestor or stem cell.

mon·o·phy·let·ic
adj.
1. Descended or derived from one original stock or source.
 groups. The RFLP tree based on general fungal primers also did not resolve species, while the basidiomycete-specific data could resolve species. In the basidiomycete-specific tree, all isolates of both G. striatum striatum /stri·a·tum/ (stri-a´tum) corpus striatum.stria´tal

stri·a·tum
n. pl. stri·a·ta
 and G. trabeum comprised monophyletic groups. Eight of nine T. versicolor versicolor /ver·si·co·lor/ (ver?si-kol´er) variegated; having a variety of colors, or changing in color.  isolates, 10 of 11 G. sepiarium isolates, and nine of 10 T. hirsuta isolates comprised monophyletic groups. Phanerochaete could not be consistently resolved into monophyletic groups at either the genetic or specific level. Our studies indicate that RFLP analysis using general fungal primers are not likely to be useful in identifying species or reconstructing phylogenetic relationships. RFLP analysis using basidiomycete-specific primers may be useful in identifying some species but not in reconstructing phylogenetic relationships although it is a simpler procedure than sequencing.

More than 95 percent of the 1.5 million homes constructed in the United States each year are framed with wood (Smith and Wu 2005) and wood composite panels, such as OSB OSB
abbr.
Order of Saint Benedict
 and plywood, which are the most common wall siding materials. Wood frequently exposed to moisture will be degraded by insects and microorganisms, thereby losing its strength and ability to serve as a construction material. In the United States, homeowners spend more than 5 billion dollars annually in replacement costs not including labor (Dost and Botsai 1990). Traditional methods to protect wood from decay have focused on the use of chemical preservatives as nonspecific, broad spectrum pesticides (Eaton and Hale 1993). Effective wood preservatives often generate environmental concerns, and many have been banned or their use restricted after they have been in service for a number of years because of unintended consequences to nontarget non·tar·get  
adj.
Not being the target, as of an agent or weapon: effects of radiotherapy on nontarget cells. 
 organisms, including humans. Wood preservatives that affect only organisms responsible for wood decay have the potential to be both more environmentally innocuous and effective in the long run. Basidiomycete fungi are the principle microbial decomposers of wood, and in order to better control and understand wood decomposition, a method to rapidly identify decay fungi and an understanding of their physiological functions in wood decay are necessary.

Fungi represent a diverse and widespread group of microorganisms whose numbers are estimated at more than 1.6 million species (Gardes and Bruns 1996). There are approximately 1,600 wood decay species (Bennet et al. 2002). Traditional methods for identifying decay fungi are difficult and time consuming. Substantial expertise is required because these fungi are traditionally classified by their basidiocarp, which is rarely present on wood products or in culture. Culture methods to identify decay fungi are also unable to differentiate mycelia of closely related species and have low sensitivity in detecting early stages of decay (Kim et al. 2005, Schmidt and Moreth 1999a). Because of their increased sensitivity and selectivity, molecular methods are currently being used to identify decay fungi. These methods include Rapid Amplified Polymorphic DNA DNA: see nucleic acid.
DNA
 or deoxyribonucleic acid

One of two types of nucleic acid (the other is RNA); a complex organic compound found in all living cells and many viruses. It is the chemical substance of genes.
 (RAPD RAPD Randomly Amplified Polymorphic DNA
RAPD relative afferent pupillary defect (ophthalmology; aka Marcus-Gunn Pupil) 
) (Hseu et al. 1996), Internal Transcribed Spacer-Restriction Fragment Length Polymorphism (ITS-RFLP) (Adair et al. 2002, Fischer and Wagner 1999, Schmidt and Moreth 1999b, Jasalavich et al. 2000), species-specific priming PCR PCR polymerase chain reaction.

PCR
abbr.
polymerase chain reaction


Polymerase chain reaction (PCR) 
 (polymerase chain reaction) (SSPP SSPP System Safety Program Plan
SSPP Society for Service Professionals in Printing
SSPP Shuttle Small Payloads Project
SSPP Sustainability: Science, Practice, & Policy
SSPP Solar Stellar Pointing Platform
SSPP Saints Peter and Paul school
) (Moreth and Schmidt 2000, Schmidt and Moreth 2000), Amplified Fragment Length Polymorphism Amplified fragment length polymorphism PCR, or "AFLP-PCR" (often AFLP), is a tool used in the study of genetics and in the practice of genetic engineering.

Amplified Fragment Length Polymorphism (AFLP
 (AFLP) (Parrent et al. 2004), Sequence-Specific Oligonucleotide Probe (SSOP SSOP Shrink Small Outline Package
SSOP Sanitation Standard Operating Procedures (USDA)
SSOP Sanitary Standard Operating Procedures
SSOP Sharescan-Open Platform (Ecopy)
SSOP Site Security Operational Procedures
) (Oh et al. 2003), rDNA-ITS region sequence analysis (White et al. 2001, Schmidt and Moreth 2002, Moreth and Schmidt 2005) and Matrix assisted laser desorption/ionization time of flight (MALDI-TOF MALDI-TOF Matrix Assisted Laser Desorption Ionization - Time of Flight ) mass spectrometry (Schmidt and Kallow 2005). Each of these methods has its own advantages and limitations including ease of application, equipment required, technical expertise, and consistency of results.

Regardless of procedures, most taxonomic analysis focuses on ribosomal DNA (rDNA). rDNA is a nuclear, multicopy gene family arranged in tandem arrays that codes for the rRNA subunits of the ribosome ribosome: see cell; nucleic acid.
ribosome

Tiny particle, the site of protein synthesis, that is present in large numbers in living cells. They occur both as free particles within cells and, in eukaryotes, as particles attached to the membranes of
 molecule. Within each array are genes coding for the small (18 S) and large (28 S) subunits. To the outside of the small and large rRNA sequences are the external transcribed spacer (ETS ETS Educational Testing Service (nonprofit private educational testing and measurement organization)
ETS Emergency Telecommunications Service
ETS Electronic Trading System
ETS Engineering (&) Technical Services
) and the intergenic spacers (IGS IGS - Internet Go Server. ). Between the small and large rRNA sequences are the internal transcribed spacer regions (ITS 1 and ITS2). The 5.8S nuclear rDNA gene lies between ITS1 and ITS2. The ITS regions are highly conserved within most species (with intraspecific in·tra·spe·cif·ic   also in·tra·spe·cies
adj.
Arising or occurring within a species: intraspecific competition.
 similarities >99%) but are variable between species, making it suitable for use in taxonomy (Gomes et al. 2002, O'Brien et al. 2005). Many primer sets are designed to target the conserved regions of fungal rRNA (Turenne et al. 1999) increasing the sensitivity and selectivity for species identification. The earliest PCR primer sets to be routinely used to amplify the fungal ITS regions were the fungal specific primer ITS1, and the fungal general primer ITS4 (White et al. 1990). These primers work well on DNA from individual organisms but do not perform well on DNA extracts containing both host plant and microbial DNA. The plant-excluding primers, ITS1F and ITS4B, were developed to be specific for fungi and basdiomycetes, respectively (Gardes and Bruns 1996)

Numerous studies have used PCR-based methods to identify fungi, but the specific primers and the number of isolates per species used in each study have varied (Diehl et al. 2004, Guidot et al. 1999, Johnston and Aust 1994, McElroy et al. 2003, Schmidt and Moreth 1999a,1999b, Walsh et al. 1995, Zaremski et al. 1999). If the identification is focused on basidiomycetes then the ITS4B primer is often used. However, the question of intraspecific variation within the ITS region for numerous wood decay basidiomycetes is unknown. Adair et al. (2002) tested 26 wood decay basidiomycetes and 20 wood inhabiting ascomycetes by ITS-RFLP using several different primer pairs including ITS4B. Of the 26 basidiomycetes evaluated, 15 were single isolate representations of the species. No intraspecific variation was detected by ITS-RFLP among the 11 basidiomycete species represented by two to four isolates. The ITS4B gene was amplified in three of the ascomycetes. RFLP of the ITS fragment (amplified with fungal general primers ITS1 and ITS4) was also able to distinguish species of Armillaria borealis, A. ostayeae, A. epistipes, A. gallica, A. medlea, A. tubescens, and A. ectypa (Chillali et al. 1998). This study used two to four isolates of each species. A comparison of ITS sequences from 27 isolates of Serpula lacrymans and four isolates of S. himantioides using the ITS4B primer found very little sequence variation within S. lacrymans, while the S. himantioides showed polymorphisms among the isolates (Hogberg and Land 2004). Kim et al. (2005) isolated 132 basidiomycete decay fungi colonizing wood playground equipment. From these cultures the fungal general primers LROR and LR3 were used to amplify the 28S region. Unique sequences were compared to GenBank sequences and 30 different fungal taxa were identified with 13 of these belonging to the polyporoid clade of the basidiomycetes. Only three species were identified based on culture morphology. Some of these studies have examined a very limited number of isolates of each species, and thus the variation within some species has not been adequately assessed. Additionally, we do not know if RFLP data and sequence data are comparable.

In this study we have reconstructed the phylogenetic tree of a select group of basidiomycete fungi using nucleotide sequences of the ITS region of the rDNA suite of genes and have compared this to trees generated from RFLP analysis using general fungal and basidiomycete-specific primers to see if the latter procedures can correctly identify multiple isolates of select wood decay fungi.

Materials and methods Fungal cultures

Fungal cultures, their sources, and use in this research project are listed in Table 1. Cultures were grown initially on Sabauraud Dextrose dextrose: see glucose.  Agar (Difco Laboratories) and subsequently in Sabauraud Dextrose Broth (Difco Laboratories) for 3 to 7 days each at 28 [degrees]C. Mycelia was filtered from the broth culture through Whatman 541 filter paper, rinsed three times with distilled water, blotted to remove excess water and stored at -70 [degrees]C until DNA extraction.

DNA isolation and PCR amplification

DNA was isolated from fungal mycelia (0.02 g) by grinding with quartz sand, and extraction following the Qiagen DNeasy Plant kit protocol. The ITS region of fungal DNA was amplified using the fungal specific primer set: ITS1-F (CTT CTT Correios (Portuguese Postal Service)
CTT Certified Technical Trainer
CTT Charity Technology Trust
CTT Cholesterol Treatment Trialists' (collaboration)
CTT Common Task Training
 GGT GGT

?-glutamyl transferase.

GGT Gammaglutamyltransferase, see there
 CAT TTA GAG GAA GTA GTA Grand Theft Auto (legal)
GTA Grand Theft Auto (video game)
GTA Greater Toronto Area (Canada)
GTA Graduate Teaching Assistant
 A) and ITS4 R (TCC TCC GCT TAT TGA TAT GC) or the basidiomycete specific primer set: ITS 1-F (CTT GGT CAT TTA GAG GAA GTA A) and ITS4B (CAG CAG 1 Chronic atrophic gastritis 2 Coronary angiography, see there  GAG ACT TGT ACA ACA - Application Control Architecture  CGG TCC AG) as described by White et al. (1990). Amplifications were performed in 100[micro]1 PCR reaction tubes containing 5[micro]1 DNA, 10[micro]10X thermophilic ther·mo·phil·ic
adj.
Requiring high temperatures for normal development, as certain bacteria.
 buffer, 8 [micro]1 Mg[Cl.sub.2], (25mM) 4 [micro]1 dNTP (10mM), 10[micro]1 (10[micro]M) ITS1-F, 10[micro]1 (10[micro]M) ITS4, 52[micro]1 dd[H.sub.2]O and 1 [micro]1 (10u/[micro]1) Taq (Promega). Amplifications occurred in an Eppendorf Mastercycler Thermal Cycler with the following program for 40 cycles: initial denaturation denaturation, term used to describe the loss of native, higher-order structure of protein molecules in solution. Most globular proteins exhibit complicated three-dimensional folding described as secondary, tertiary, and quarternary structures.  temperature 94 [degrees]C for 1 minute 30 seconds, melt temperature 95 [degrees]C for 35 seconds, annealing temperature 55 [degrees]C for 55 seconds, extending temperature of 72 [degrees]C for 1 minute, final extension temperature 72 [degrees]C for 10 minutes, hold temperature 4 [degrees]C (Jasalavich et al. 2000). The ITS bands were identified by gel electrophoresis on a 2 percent agarose. Molecular weights of each ITS fragment were determined using GelPro Express software and a 100 bp ladder.

Restriction digestion of PCR products

The fungal ITS fragments were digested with four restriction enzymes: Hinf1, HaeIII, Alu, and TaqI (Promega) following manufacturers recommendations of 37 [degrees]C for 4 hours (Hinf1, HaeIII and Alu) and 65 [degrees]C for 2 hours for TaqI. Digested bands were separated by gel electrophoresis using 2.5 percent high resolution agarose gel in 1X TBE running buffer amended with 0.002 percent ethidium bromide. Bands were visualized under a transillunminator box with UV light. Gels were photographed using a Polaroid camera and visualized with PhotoMax Pro[TM] software. Molecular weights of the digested bands were calculated using GelPro Express software and a 50 bp ladder. At least three replications per fungal isolate were run.

RFLP data analyses

RFLP profiles for each restriction enzyme were converted to binary data (presence or absence of a fragment for each sample) in Excel using 50bp binning. A simple matching similarity matrix for each restriction enzyme was calculated for samples and analyzed with hierarchical cluster analysis in SYSTAT (Wilkinson 1983) and PHYLIP PHYLIP Phylogeny Inference Package (genetics software)  (Felsenstein 2005). Trees were produced with YreeView (Page 1996).

DNA sequencing

Excess primers and buffers were removed from the amplified ITS fragment according to procedures given in the Mo Bio PCR DNA purification kit. DNA concentration, as determined by fluorescence, was done according to procedures in the Sigma DNA Quantification Kit and ranged between 2 ng/ [micro]l and 100 ng/[micro]1. The fungal ITS fragment was prepared for sequencing according to the Beckman CEQ DTCS DTCS Design Technology Consulting Services (Dallas, Texas)
DTCS Senior Chief Dental Technician (Naval Rating)
DTCS DSCS Tactical Control Subsystem
DTCS Distributed Table Construction Scheme
 kit. The target DNA concentration was 45 ng/50 fmol. Fragments were sequenced with a Beckman CEQ 2000XL capillary sequencer.

Sequence data analysis and creation of phylogenic tree

ITS sequence data were analyzed by the CEQ[TM] 8000 Genetic Analysis System (Beckman Coulter) software. The forward and reverse sequences for each fungal species were aligned with Clustal W (Kumar et al. 2001) validated visually and a consensus sequence was generated also with Clustal W. The identity of the consensus sequence was confirmed using BLAST search to known sequences in NCBI NCBI National Center for Biotechnology Information (NIH)
NCBI National Coalition Building Institute
NCBI National Council for the Blind of Ireland (Dublin, Ireland) 
 Genbank. A phylogenetic tree based on maximum likelihood with 100 bootstrap replications was constructed using DAMBE (Xia 2000, Xia and Xie 2001). Paecilomyces sp. was used as an out-group. Neighbor-joining and maximum parsimony trees were also constructed for comparison but not shown.

Results and discussion

Sequence data of ITS fragments of selected wood decay fungi were used to generate a phylogenetic tree for comparison of relatedness among these fungi to relatedness in phylogenetic trees generated from two restriction fragment length polymorphism (RFLP) methods on the fungal ITS fragments. There were 15 wood decay fungal samples used to generate sequence data, 33 fungal samples to generate RFLP-GEN data, and 47 fungal samples to generate RFLP-B. Some of the fungal isolates would not adequately sequence. Several different sequencing preparations were attempted, but all failed to provide an acceptable sequence. The sequence of several isolates from cultures did not correspond to the expected species and these were omitted from the study. Trametes hirsuta 46211 (THE) appeared as an outlier from the other T. hirsuta isolates in the three phylogenetic trees. This isolate was identified through GenBank as T. hirsuta. The other T. hirsuta isolates were identified through GenBank as a basidiomycete. P. chrysosporium 62777 (PCE PCE pseudocholinesterase; see cholinesterase.
erythromycin

Apo-Erythro (CA), Apo-Erythro-EC, Diomycin (CA), E-Base, E-Mycin, Erybid (CA), Erymax (UK), Ery-Tab, Erythromid (CA), PCE (CA), Rommix (UK), Tiloryth (UK)

) was identified as P. sordia.

The ITS-based phylogenetic tree using maximum likelihood revealed three well-supported genera, Trametes, Phanerochaete, and Gloeophyllum, with bootstrap values of 75 or greater (Fig. 1). Trametes and Phanerochaete were sister taxa, and Gloeophyllum was a sister taxon to the Trametes/ Phanerochaete clade. Other phylogenetic analyses showed similar patterns with some variation. These three genera were well supported by neighbor-joining analysis (data not shown), but the clade containing both Trametes and Phanerochaete was not supported. Maximum parsimony analysis showed well-supported Trametes and Gloeophyllum genera, but a monophyletic Phanerochaete genus was not supported since one Phanerochaete species was a sister taxon to the Trametes genus and the other Phanerochaete species was a sister taxon to the Gloeophyllum genus (data available from corresponding author).

Within Trametes one species, T. versicolor, was well supported by maximum likelihood analysis with a bootstrap value of 100 (Fig. 1). T. hirsuta could not be resolved into a single clade. Isolates A, D, G, and F constituted one monophyletic group, but isolate E was a sister taxon to the rest of the entire Trametes clade. Within the Gloeophyllum genus, neither species (G. sepiarium, G. striatum) could be separated into monophyletic clades. Regardless of phylogenetic analysis employed, basidiomycete species could not be resolved from ITS sequences alone, but maximum likelihood and neighbor-joining analyses successfully resolved genera.

[FIGURE 1 OMITTED]

RFLP-based cluster analyses of trees generated from general fungal primers and basidiomycete-specific primers are shown in Figures 2 and 3, respectively. Neither set of cluster analyses could resolve the three genera into monophyletic groups. The tree based on general fungal primers (Fig. 2) also did not resolve species well. The tree based on Basidiomycete-specific primers (Fig. 3) resolved species much better. All isolates of both G. striatum and G. trabeum comprised monophyletic groups. Eight of nine T. versicolor isolates, 10 of 11 G. sepiarium isolates, and 9 of 10 T. hirsuta isolates comprised monophyletic groups. Phanerochaete could not be consistently resolved into monophyletic groups at either the generic or specific level. In contrast to Hogberg and Land (2004) only two of the species tested in this study were resolved by sequence data as monophyletic groups (T. versicolor and P. chrysosporium). Identification of unknowns from environmental samples, such as in the study by Kim et al. (2005), assumes each species resolves as monophyletic groups. Our data do not support this assumption for all species.

[FIGURE 2 OMITTED]

Based on RFLP-GEN and RFLP-B phylogenetic trees compared to the sequence (SEQ) tree, results indicated that a very similar clustering pattern exists for Trametes among the three trees. Trametes hirsuta isolates THA THA Total hip arthroplasty. See Total hip replacement. , THD and THG clustered together in the same pattern in RFLP-Gen, RFLP-B, and SEQ trees. T. hirsuta, THE appeared as a sister group to the other Trametes in all three phylogenetic trees. T. hirsuta THF THF tetrahydrofolic acid.

THF

tetrahydrofolic acid.
 grouped with the other T. hirsuta in the RFLP-B and sequence trees but grouped with isolates of T. versieolor in the RFLPGEN tree. The three isolates of Trametes versicolor (TVE, TVF, TVH TVH Total vaginal hysterectomy. See Vaginal hysterectomy. ) clustered in the same clade in all three trees.

There were seven isolates of Phanerochaete chrysosporium (PC) evaluated in the RFLP-B and five in the RFLP-GEN phylogenetic trees but only two isolates in the sequence phylogenetic tree because of a lack of acquiring usable sequence data in spite of several attempts. Phanerochaete chrysosporium clustered separately from Trametes in all trees. In the RFLP-GEN tree, four of the five PC isolates clustered together while the fifth, PCE, clustered more with P. sanguinea, PSGA PSGA Polymer Stud Grid Array (chip scale package)
PSGA Pharmaceutical Sourcing Group Americas
PSGA Puget Sound Grantwriters Association (Seattle, WA)
PSGA Pedal Steel Guitar Association
 and PSGB PSGB Primate Society of Great Britain
PSGB Pharmaceutical Society of Great Britain
. PSGC PSGC Philippine Standard Geographic Code  clustered as a sister elade within the Phanerochaete clade and was determined to be 99.8 percent similar to P. sordida (AY219381.1) by GenBank Blast analysis. However, no P. sorida isolates were sequenced to confirm this observation. Gloeophyllum sepiarium 32892 (GSEPH) appeared with the Phanerochaete clade but was later determined to be P. chrysosporium AFTOL 776 (92.2% similarity) by sequence analysis. In the RFLP-B phylogenetic tree, all PC isolates except PCE (which clustered in the same clade as Trametes versicolor), appeared unrelated to each other or any other isolates evaluated, The only two PC isolates, PCA and PCB, successfully sequenced did cluster in the same clade and was well supported by a bootstrap value of 100.

[FIGURE 3 OMITTED]

The data for Gloeophyllum striatum and G. sepiarium did not result in a distinct clustering pattern in the RFLP-GEN or SEQ phylogenetic trees. There was an insufficient number of isolates of G. trabeum analyzed by either RFLP-GEN or sequence methods. In the RFLP-B tree, the three species of Gloeophyllum did form a distinct clade with each other with the exception of isolate GSEPF which formed a sister clade with other Gloeophyllums.

Identification of wood decay fungi has challenged researchers for many years. Successful identification of wood decay fungi will increase as more researchers add to the databases. For this to occur there are research needs for 1) additional nucleotide sequences to generate more robust phylogenetic trees with greater potential to resolve both genera and species, and 2) inclusion of multiple isolates of each species. Our studies indicate that RFLP analysis using general fungal primers are not likely to be useful in identifying species or reconstructing phylogenetic relationships. RFLP analysis using Basidiomycete-specific primers may be useful in identifying some species but not in reconstructing phylogenetic relationships although it has an advantage that it is a simpler procedure compared to sequencing. RFLP may be more useful if additional basidiomycete-specific primers are incorporated.

Literature cited

Adair, S., S.H. Kim, and C. Brueil. 2002. A molecular approach for early monitoring of decay basidiomycetes in wood chips. FEMS Microbiol. Lett. 211:117-122.

Bennet, J.W., K.G. Wunch, and B.D. Faison. 2002. Use of fungi in Biodegradation. In: Manual of Environmental Microbiology. 2nd Ed. Christon J. Hurst. pp. 960-971

Chillai, M., H. Idder-Ighili, J.J. Guiltaumin, C. Mohammed, B.L. Escarmant, and B. BoRon. 1998. Variation in the ITS and IGS regions of ribosomal DNA among the biological species of European Armillaria. Mycol. Res. 102:533-540.

Diehl, S.V., T.C. McElroy and M.L. Prewitt. 2004. Development and implementation of a DNA-RFLP database for wood decay and wood associated fungi. The Inter. Res. Group on Wood Preservation. IRG 35, IRG/WP 04-10527:1-18.

Dost, W.A. and E.E. Botsai. 1990. Wood: Detailing for Performance. GRDA GRDA Grand River Dam Authority  Publications, Mill Valley, California. pp. 13.1-13.4

Eaton, R.A. and M.D.C. Hale. 1993. Wood-decay, pest, and protection. Chapman and Hall Chapman and Hall was a British publishing house, founded in the first half of the 19th century by Edward Chapman and William Hall. Upon Hall's death in 1847, Chapman's cousin Frederic Chapman became partner in the company, of which he became sole manager upon the retirement of . London.

Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Dept. of Genome Sciences, Univ. of Washington, Seattle.

Fischer, M. and T. Wagner. 1999. RFLP analysis as a tool for identification of lignicolous basidiomycetes: European polypores. Eur. J. Forest Pathol. 29:205-304.

Gardes, M. and T.D. Bruns. 1996. ITS-RFLP Matching for identification of fungi. Methods Mol. Biol. 50:177-186.

Guidot, A., E. Lumini, J.-C. Debaud, and R. Marmeisse. 1999. The nuclear ribosomal DNA intergenic spacer as a target sequence to study intraspecific diversity of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum directly on Pinus root systems. Appl. Environ. Microbiol. 65:903-909.

Gomes, E.A., M.C. Kasaya, E.G. deBarros, A.C. Borgs, and E.F. Araujo. 2002. Polymorphism in the internal transcribed spacer (ITS) of the ribosomal DNA of 26 isolates of ectomycorrhizal fungi. Genet. Mol. Biol. 25(4):477-483.

Hogberg, N. and C.J. Land. 2004. Identification of Serpula lacrymans and other decay fungi in construction timber by sequencing of ribosomal DNA--A practical approach. Holfzorschung 58:199-204.

Hseu, R.S., H.H. Wang, H.F. Wang, and J.M. Moncalvo. 1996. Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences. Appl. Environ. Microbiol. 62(4):1354-1363.

Jasalavich, C., A. Ostrotsky, and J. Jellison. 2000. Detection and identification of decay fungi in spruce wood by restriction fragment length polymorphism analysis of amplified genes encoding rRNA. Appl. Environ. Microbiol. 66(11):4725-4734.

Johnston, C.G. and S.D. Aust. 1994. Detection of Phanerochaete chrysosporium in soil by PCR and restriction enzyme analysis. Appl. Environ. Microbiol. 60:2350-2354.

Kim, G.H., Y.W. Lim, Y.S. Song, and J.J. King. 2005. Decay fungi from playground wood products in service using 28S rDNA sequence analysis. Holzforschung 59:459-466.

Kumar, S., K. Tamura, I.B. Jakolosen, and M. Nei. 2001. MEGA2: Molecular Evolutional Genetics Analysis Software. Bioinformatics 17(12):1244-1245.

McElroy, T.C., L. Prewitt and S.V. Diehl. 2003. A comparison of fatty acid and molecular profiles for identification of wood colonizing basidomycota. Inter. Res. Group on Wood Preservation IRG 34, IRG/WP 03-20278:1-12

Moreth, U. and O. Schmidt. 2000. Identification of indoor rot fungus by taxon specific primer polymerase chain reaction. Holzfurschung 54:1-8. -- and --. 2005. Investigations on ribosomal DNA of indoor wood decay fungi for their characterization and identification. Holzforschung 59:90-93.

O'Brien, H.E., J.L. Parrent, J.A. Jackson, J.M. Moncalvo, and R. Vilgalys. 2005. Fungal communities' analysis by large-scale sequencing of environmental samples. Environ. Microbiol. 71:5544-5550.

Oh, S., D.P. Kamdem, D.E. Keathley, and K.H. Han. 2003. Detection and species identification of wood-decaying fungi by hybridization hybridization /hy·brid·iza·tion/ (hi?brid-i-za´shun)
1. crossbreeding; the act or process of producing hybrids.

2. molecular hybridization

3.
 of immobilized sequence-specific oliogonueleotide probes with PCR-amplified fungal ribosomal DNA internal transcribed spacers. Holzforschung 57:346-352.

Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.

Parrent, J.L., M. Garelotto, and G.S. Gilbert. 2004. Population genetic structure of the polypore Datrobnia caperata in fragmented mangrove forest. Mycol. Res. 108(4):403-409.

Schmidt, O. and U. Moreth. 1999a. Identification of the Dry Rot Fungus, Serpula lacrymans, and the wild merulis S. himantioides by amplified ribosomal DNA restriction analysis (ARDRA ARDRA Amplified RDNA Restriction Analysis ). Holzforschung 53: 123-128.

-- and --. 1999b. rDNA-ITS sequence of Serpula lacrymans and other important indoor rot fungi and taxon-specific priming for their detection. IRG/WP 99-10298

-- and --. 2000. Species-specific priming PCR in the rDNA-ITS regions as a diagnostic tool for Serpula lacrymans. Mycol. Res. 104:69-72.

-- and--. 2002. Data bank of rDNA-ITS sequences from building-rot fungi for their identification. Wood Sci. and Tech. 36:429-433.

-- and W. Kallow. 2005. Differentiation of indoor wood decay fungi with MADLI-TOF mass spectrometry. Holzfurschung 59:374377.

Smith, W.R. and Q. Wu. 2005. Durability improvement for structural wood composites through chemical treatments: Current state of the art. Forest Prod. J. 55(2):8-17.

Turenne, C.Y., S.E. Sanche, D.J. Hobart, J.A. Karlowsky, and A.M. Kabane. 1999. Rapid identification of fungi using the ITS2 genetic region and an automatic fluorescence capillary electrophoresis system. J. Clin. Microbiol. 37(6):1846-1851.

Walsh, T.J., A. Franscesconi, M. Kasai, and S.J. Chanock. 1995. PCR and single-strand conformation polymorphism for recognition of medically important opportunistic fungi. J. Clin. Microbiol. 33:3216-3220.

White, T.J., T. Bruns, S. Lee, and J.W. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications Edited by Innis, M.A., Gelfand D.H., Sninsky H.H., White T.J. New York Academic Press Inc. p.315-322.

White, N.A., P.K. Dehal, J.M. Duncan, N.A. Williams, J.S. Gartland, J.W. Palfreyman, and D.E.L. Cooke. 2001. Molecular analysis of intraspecific variation between building and "wild" isolates of Serpula lacrymans and their relatedness to S. himantioides. Mycol. Res. 105(4): 447-452.

Wilkinson, L. 1983: SYSTAT: System Statistics. Proc. of the American Statistical Assoc., Statistical Computing Section.

Xia, X. and Z. Xie. 2001. DAMBE: Data analysis in molecular biology and evolution. J. Hered. 92:371-373.

--. 2000. Data analysis in molecular biology and evolution. Kluwer Academic publishers, Boston. pp. 276.

Zaremski, A., M. Ducousso, Y. Prin, and D. Fouquet. 1999. CIRAD CIRAD Centre de Coopération Internationale en Recherche Agronomique pour le Développement (French Agricultural Research Centre for International Development)  create a molecular database of wood-decaying fungi, (abstract), IRG/WP 99-10298.

M. Lynn Prewitt * Susan V. Diehl * Thomas C. McElroy Walter J. Diehl

* Forest Products Society Member.

The authors are, respectively, Assistant Research Professor and Associate Professor, Dept. of Forest Products, Mississippi State Univ., Mississippi State, Mississippi (lprewitt@cfr.msstate.edu; sdiehl@cfr.msstate.edu); Assistant Professor, Kennesaw State Univ., Kennesaw, Georgia (tmcelro@kennesaw.edu); and Professor, Mississippi State Univ., Mississippi State, Mississippi (wdiehl@biology.msstate.edu). This work was funded by grants from the USDA/Wood Utilization Research and the Life Sciences and Biotechnology Inst. (LSBI LSBI Low-Speed Binary Interface ) Mississippi State Univ. This paper has been approved as FWRC 404. This paper was received for publication in February 2007. Article No. 10312.
Table 1.--Fungal species and codes used in generating
phylogenetic trees. Checks indicate which isolate was used in
which analysis. RFLP BASDIO indicates the RFLP tree generated
using the basidiomycete specific primers. RFLP GEN
indicates the RFLP tree generated using the general fungal
primers. SEQUENCE indicates the tree generated using sequence data.

                                            RFLP      RFLP
Species                   Source   Code    BASDIO     GEN      Sequence

T. hirsuta 66131            a      THF     [check]   [check]   [check]
T. hirsuta 46211            a      THE     [check]   [check]   [check]
T. hirsuta 34679            b      THD     [check]   [check]   [check]
T. hirsuta 10666            a      THG     [check]   [check]   [check]
T. hirsuta DR277            a      THA     [check]   [check]   [check]
T. hirsuta RLG              a      THB     [check]
T. hirsuta 8591             a      THC     [check]
T. hirsuta 10700            b      THH     [check]
T. hirsuta 105981           b      THI     [check]
T. hirsuta 125074           b      THJ     [check]
T. versicolor 64311         a      TVF     [check]   [check]   [check]
T. versicolor 60985         a      TVE     [check]   [check]   [check]
T. versicolor 12679         a      TVH     [check]   [check]   [check]
T. versicolor 32745         a      TVA     [check]
T. versicolor 34578         a      TVB     [check]
T. versicolor 34584         a      TVC     [check]
T. versicolor 42462         a      TVD     [check]
T. versicolor 11235         a      TVG     [check]
T. versicolor DR-EST        c      TVI     [check]
P. chrysosporium 102169     a      PCG     [check]   [check]
P. chrysosporium 34541      b      PCB     [check]   [check]   [check]
P. chrysosporium 48747      a      PCD     [check]   [check]
P. chrysosporium 32629      a      PCA     [check]   [check]   [check]
P. chrysosporium 62777      a      PCE     [check]   [check]
P. chrysosporium 48746      a      PCC     [check]
P. chrysosporium 62778      a      PCF     [check]
P. sanguinea 7524           b      PSGA              [check]
P. sanguinea 9865           b      PSGB              [check]
P. sanguinea 102375         b      PSGC              [check]
G. striatum 32520           a      GSTH              [check]
G. striatum 102563          b      GSTI              [check]
G. striatum 32521           a      GSTA    [check]   [check]   [check]
G. striatum 7305            b      GSTE    [check]   [check]   [check]
G. striatum 64699           b      GSTF    [check]   [check]   [check]
G. striatum BKW-003         b      GSTB    [check]
G. striatum CR04            b      GSTD    [check]
G. sepiarium 28094          a      GSEPE   [check]   [check]
G. sepiarium 12677          a      GSEPD   [check]   [check]
G. sepiarium 9419           a      GSEPA   [check]   [check]   [check]
G. sepiarium 60231          a      GSEPB   [check]   [check]   [check]
G. sepiarium 64312          a      GSEPC   [check]   [check]
G. sepiarium 32892          a      GSEPH   [check]   [check]
G. sepiarium 32518          a      GSEPF   [check]
G. sepiarium 32519          a      GSEPG   [check]
G. sepiarium 46278          a      GSEPI   [check]
G. sepiarium 14159          a      GSEPK   [check]
G. sepiarium DR275          c      GSEPJ   [check]
G. trabeum 105470           b      GTE               [check]
G. trabeum 101508           b      GTC     [check]   [check]
G. trabeum Dietz            b      GTF               [check]
G. trabeum 32084            a      GTG               [check]
G. trabeum 32743            a      GTH               [check]
G. trabeum 8715             a      GTI               [check]
G. trabeum 11539            a      GTA     [check]
G. trabeum 13021            a      GTB     [check]
G. trabetun 274             c      GTD     [check]

a American Type Culture Collection (ATCC).

b USDA Forest Products Laboratory, Madison, Wisconsin.

c Michigan Technological University, Dr. Dana Richtor.
COPYRIGHT 2008 Forest Products Society
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 2008 Gale, Cengage Learning. All rights reserved.

 Reader Opinion

Title:

Comment:



 

Article Details
Printer friendly Cite/link Email Feedback
Title Annotation:internal transcribed spacer
Author:Prewitt, M. Lynn; Diehl, Susan V.; McElroy, Thomas C.; Diehl, Walter J.
Publication:Forest Products Journal
Article Type:Author abstract
Date:Apr 1, 2008
Words:4759
Previous Article:Effects of wood species and enzyme production on lignocellulose degradation during the biodegradation of three native woods by Trametes versicolor.
Next Article:Influence of decay fungi, construction characteristics, and environmental conditions on the quality of wooden check-dams.
Topics:

Terms of use | Copyright © 2014 Farlex, Inc. | Feedback | For webmasters