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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Artikel i vetenskaplig tidskrift
Författare CL Schoch
KA Seifert
S Huhndorf
Vincent Robert
JL Spouge
CA Levesque
W Chen
E Bolchacova
K Voigt
PW Crous
AN Miller
MJ Wingfield
MC Aime
KD An
FY Bai
RW Barreto
D Begerow
MJ Bergeron
M Blackwell
T Boekhout
M Bogale
N Boonyuen
AR Burgaz
B Buyck
L Cai
Q Cai
G Cardinali
P Chaverri
BJ Coppins
A Crespo
P Cubas
C Cummings
U Damm
ZW de Beer
GS de Hoog
R Del-Prado
B Dentinger
J Diéguez-Uribeondo
PK Divakar
B Douglas
M Dueñas
TA Duong
U Eberhardt
JE Edwards
MS Elshahed
K Fliegerova
M Furtado
M García
ZW Ge
GW Griffith
K Griffiths
JZ Groenewald
M Groenewald
M Grube
M Gryzenhout
LD Guo
F Hagen
S Hambleton
RC Hamelin
K Hansen
P Harrold
G Heller
C Herrera
K Hirayama
Y Hirooka
HM Ho
K Hoffmann
V Hofstetter
F Högnabba
PM Hollingsworth
SB Hong
K Hosaka
J Houbraken
K Hughes
S Huhtinen
KD Hyde
T James
EM Johnson
JE Johnson
PR Johnston
EB Jones
LJ Kelly
PM Kirk
DG Knapp
U Kõljalg
GM Kovács
CP Kurtzman
S Landvik
SD Leavitt
AS Liggenstoffer
K Liimatainen
L Lombard
JJ Luangsa-Ard
HT Lumbsch
H Maganti
SS Maharachchikumbura
MP Martin
TW May
AR McTaggart
AS Methven
W Meyer
J-M Moncalvo
S Mongkolsamrit
LG Nagy
R. Henrik Nilsson
T Niskanen
I Nyilasi
G Okada
I Okane
I Olariaga
J Otte
T Papp
D Park
T Petkovits
R Pino-Bodas
W Quaedvlieg
HA Raja
D Redecker
TL Rintoul
C Ruibal
JM Sarmiento-Ramírez
I Schmitt
A Schüßler
C Shearer
K Sotome
FO Stefani
S Stenroos
B Stielow
H Stockinger
S Suetrong
SO Suh
GH Sung
M Suzuki
K Tanaka
L Tedersoo
MT Telleria
E Tretter
WA Untereiner
H Urbina
C Vágvölgyi
A Vialle
TD Vu
G Walther
QM Wang
Y Wang
BS Weir
M Weiß
MM White
J Xu
R Yahr
ZL Yang
A Yurkov
JC Zamora
N Zhang
WY Zhuang
D Schindel
Publicerad i Proceedings of the National Academy of Sciences of the United States of America
Volym 109
Nummer/häfte 16
Sidor 6241-6246
ISSN 1091-6490
Publiceringsår 2012
Publicerad vid Institutionen för biologi och miljövetenskap
Sidor 6241-6246
Språk en
Länkar www.pnas.org/content/109/16/6241.fu...
Ämnesord Fungi ; barcoding ; ITS
Ämneskategorier Mikrobiologi, Morfologi, Bioinformatik och systembiologi, Biologisk systematik, Medicinsk mikrobiologi

Sammanfattning

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

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