PMID- 19465521
OWN - NLM
STAT- MEDLINE
DCOM- 20090928
LR  - 20240317
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 75
IP  - 14
DP  - 2009 Jul
TI  - Selection of enzymes for terminal restriction fragment length polymorphism 
      analysis of fungal internally transcribed spacer sequences.
PG  - 4747-52
LID - 10.1128/AEM.00568-09 [doi]
AB  - Terminal restriction fragment length polymorphism (TRFLP) profiling of the 
      internally transcribed spacer (ITS) ribosomal DNA of unknown fungal communities 
      is currently unsupported by a broad-range enzyme-choosing rationale. An in silico 
      study of terminal fragment size distribution was therefore performed following 
      virtual digestion (by use of a set of commercially available 135 type IIP 
      restriction endonucleases) of all published fungal ITS sequences putatively 
      annealing to primers ITS1 and ITS4. Different diversity measurements were used to 
      rank primer-enzyme pairs according to the richness and evenness that they showed. 
      Top-performing pairs were hierarchically clustered to test for data dependency. 
      The enzyme set composed of MaeII, BfaI, and BstNI returned much better results 
      than randomly chosen enzyme sets in computer simulations and is therefore 
      recommended for in vitro TRFLP profiling of fungal ITSs.
FAU - Alvarado, Pablo
AU  - Alvarado P
AD  - Departamento de Biologia Vegetal, Universidad de Alcala, Ctra. Madrid-Barcelona 
      km 33.6, Alcala de Henares, 28871 Madrid, Spain.
FAU - Manjon, Jose L
AU  - Manjon JL
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20090522
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
RN  - 0 (DNA, Fungal)
RN  - 0 (DNA, Ribosomal Spacer)
RN  - EC 3.1.21.- (DNA Restriction Enzymes)
SB  - IM
MH  - Computational Biology
MH  - DNA Fingerprinting/*methods
MH  - DNA Restriction Enzymes/*metabolism
MH  - DNA, Fungal/genetics/*metabolism
MH  - DNA, Ribosomal Spacer/genetics/*metabolism
MH  - Fungi/*classification/*genetics
MH  - Mycological Typing Techniques/methods
MH  - *Polymorphism, Restriction Fragment Length
PMC - PMC2708443
EDAT- 2009/05/26 09:00
MHDA- 2009/09/29 06:00
PMCR- 2010/01/01
CRDT- 2009/05/26 09:00
PHST- 2009/05/26 09:00 [entrez]
PHST- 2009/05/26 09:00 [pubmed]
PHST- 2009/09/29 06:00 [medline]
PHST- 2010/01/01 00:00 [pmc-release]
AID - AEM.00568-09 [pii]
AID - 0568-09 [pii]
AID - 10.1128/AEM.00568-09 [doi]
PST - ppublish
SO  - Appl Environ Microbiol. 2009 Jul;75(14):4747-52. doi: 10.1128/AEM.00568-09. Epub 
      2009 May 22.