Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review.
Identifieur interne : 002F73 ( Main/Corpus ); précédent : 002F72; suivant : 002F74Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review.
Auteurs : I A Dickie ; R G FitzjohnSource :
- Mycorrhiza [ 0940-6360 ] ; 2007.
English descriptors
- KwdEn :
- Colony Count, Microbial (MeSH), DNA Primers (MeSH), DNA Restriction Enzymes (MeSH), DNA, Fungal (genetics), DNA, Ribosomal Spacer (MeSH), Databases, Genetic (MeSH), Mycological Typing Techniques (methods), Mycorrhizae (classification), Mycorrhizae (genetics), Polymerase Chain Reaction (methods), Polymorphism, Restriction Fragment Length (MeSH), Species Specificity (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal.
- chemical : DNA Primers, DNA Restriction Enzymes, DNA, Ribosomal Spacer.
- classification : Mycorrhizae.
- genetics : Mycorrhizae.
- methods : Mycological Typing Techniques, Polymerase Chain Reaction.
- Colony Count, Microbial, Databases, Genetic, Polymorphism, Restriction Fragment Length, Species Specificity.
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) is an increasingly widely used technique in mycorrhizal ecology. In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. Although potentially less accurate than some other methods such as clone libraries, the high throughput of database T-RFLP permits much greater replication and may, therefore, be preferable for many ecological questions, particularly when combined with other techniques such as cloning.
DOI: 10.1007/s00572-007-0129-2
PubMed: 17429700
Links to Exploration step
pubmed:17429700Le document en format XML
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In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. Although potentially less accurate than some other methods such as clone libraries, the high throughput of database T-RFLP permits much greater replication and may, therefore, be preferable for many ecological questions, particularly when combined with other techniques such as cloning.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17429700</PMID><DateCompleted><Year>2007</Year><Month>11</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0940-6360</ISSN><JournalIssue CitedMedium="Print"><Volume>17</Volume><Issue>4</Issue><PubDate><Year>2007</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Mycorrhiza</Title><ISOAbbreviation>Mycorrhiza</ISOAbbreviation></Journal><ArticleTitle>Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: a methods review.</ArticleTitle><Pagination><MedlinePgn>259-270</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00572-007-0129-2</ELocationID><Abstract><AbstractText>Terminal restriction fragment length polymorphism (T-RFLP) is an increasingly widely used technique in mycorrhizal ecology. In this paper, we review the technique as it is used to identify species of mycorrhizal fungi and distinguish two different versions of the technique: peak-profile T-RFLP (the original version) and database T-RFLP. We define database T-RFLP as the use of T-RFLP to identify individual species within samples by comparison of unknown data with a database of known T-RFLP patterns. This application of T-RFLP avoids some of the pitfalls of peak-profile T-RFLP and allows T-RFLP to be applied to polyphyletic functional groups such as ectomycorrhizal fungi. The identification of species using database T-RFLP is subject to several sources of potential error, including (1) random erroneous matches of peaks to species, (2) shared T-RFLP profiles across species, and (3) multiple T-RFLP profiles within a species. A mathematical approximation of the risk of the first type of error as a function of experimental parameters is discussed. 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IdType="pubmed">17226045</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2006 Jan;55(1):57-67</Citation><ArticleIdList><ArticleId IdType="pubmed">16420615</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2006 Sep;57(3):409-19</Citation><ArticleIdList><ArticleId IdType="pubmed">16907755</ArticleId></ArticleIdList></Reference><Reference><Citation>Microb Ecol. 2001 Dec;42(4):495-505</Citation><ArticleIdList><ArticleId IdType="pubmed">12024232</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2006 Sep;66(3):512-20</Citation><ArticleIdList><ArticleId IdType="pubmed">16564584</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2005 Apr;166(1):251-62</Citation><ArticleIdList><ArticleId IdType="pubmed">15760368</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2001 Aug;10(8):1855-71</Citation><ArticleIdList><ArticleId IdType="pubmed">11555231</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2004 Oct;14(5):283-93</Citation><ArticleIdList><ArticleId IdType="pubmed">14530929</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2000 Jun 1;32(3):241-247</Citation><ArticleIdList><ArticleId IdType="pubmed">10858583</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2004 Mar 1;47(3):397-404</Citation><ArticleIdList><ArticleId IdType="pubmed">19712328</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2002 Mar;11(3):571-81</Citation><ArticleIdList><ArticleId IdType="pubmed">11928709</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycol Res. 2005 Feb;109(Pt 2):212-26</Citation><ArticleIdList><ArticleId IdType="pubmed">15839105</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2006 Nov;16(8):525-31</Citation><ArticleIdList><ArticleId IdType="pubmed">16983569</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Microbiol. 2004 Aug;6(8):769-79</Citation><ArticleIdList><ArticleId IdType="pubmed">15250879</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Microbiol. 2005 Nov;7(11):1743-54</Citation><ArticleIdList><ArticleId IdType="pubmed">16232289</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2005 Jan;165(1):305-16</Citation><ArticleIdList><ArticleId IdType="pubmed">15720642</ArticleId></ArticleIdList></Reference><Reference><Citation>Yeast. 1993 Jan;9(1):53-8</Citation><ArticleIdList><ArticleId IdType="pubmed">8442387</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2006;169(1):169-78</Citation><ArticleIdList><ArticleId IdType="pubmed">16390428</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2000 Jul;66(7):2943-50</Citation><ArticleIdList><ArticleId IdType="pubmed">10877790</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2005 Jul;15(5):365-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15772816</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Microbiol. 2005 Dec;7(12):1952-66</Citation><ArticleIdList><ArticleId IdType="pubmed">16309393</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2002 Dec 1;42(3):327-37</Citation><ArticleIdList><ArticleId IdType="pubmed">19709292</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Microbiol. 1999 Jun;2(3):323-7</Citation><ArticleIdList><ArticleId IdType="pubmed">10383864</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2003 Nov;12(11):3085-95</Citation><ArticleIdList><ArticleId IdType="pubmed">14629388</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2003 Jul;54(1):121-5</Citation><ArticleIdList><ArticleId IdType="pubmed">12732430</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2000 Sep 28;407(6803):506-8</Citation><ArticleIdList><ArticleId IdType="pubmed">11029000</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Issues Intest Microbiol. 2001 Mar;2(1):17-25</Citation><ArticleIdList><ArticleId IdType="pubmed">11709853</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2006 Mar;15(3):873-82</Citation><ArticleIdList><ArticleId IdType="pubmed">16499709</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2003 Aug;13(4):191-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12938031</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2005 Jan;15(1):1-6</Citation><ArticleIdList><ArticleId IdType="pubmed">14669095</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1997 Nov;63(11):4516-22</Citation><ArticleIdList><ArticleId IdType="pubmed">9361437</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2003 Jan;69(1):327-33</Citation><ArticleIdList><ArticleId IdType="pubmed">12514012</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2007;173(3):611-20</Citation><ArticleIdList><ArticleId IdType="pubmed">17244056</ArticleId></ArticleIdList></Reference><Reference><Citation>Ecology. 2007 Mar;88(3):559-66</Citation><ArticleIdList><ArticleId IdType="pubmed">17503582</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2006;170(2):381-90</Citation><ArticleIdList><ArticleId IdType="pubmed">16608462</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2003 Feb;69(2):926-32</Citation><ArticleIdList><ArticleId IdType="pubmed">12571013</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20</Citation><ArticleIdList><ArticleId IdType="pubmed">16880384</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2003 Nov;69(11):6768-76</Citation><ArticleIdList><ArticleId IdType="pubmed">14602639</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2002 Sep;68(9):4370-6</Citation><ArticleIdList><ArticleId IdType="pubmed">12200289</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2003 Jul 1;45(2):105-14</Citation><ArticleIdList><ArticleId IdType="pubmed">19719621</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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