Transcript Document

Animals
80,000
Plants
60,000
40,000
Fungi
20,000
The Fungal Community: Its Organization and Role in the Ecosystem,
Third Edition
Edited by John Dighton, James F White Jr. and Peter Oudemans
CRC Press
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GenBank Taxonomy nodes
100,000
“Many of our unidentifiable sequences may represent novel lineages with no representatives
known from cultures or fruiting bodies, but almost all SSU sequences clustered with known
fungal groups in phylogenetic analyses, suggesting that they represent known fungi
which are not yet in the ITS database.”
O’Brien et al. 2005.
800k+ specimens
100+ in GenBank
GenBank
?
Kew
9.5k+ species
(Nilsson et al. ‘06)
Nature
5+ million fungal species
(O’Brien et al. ‘05)
“Closing the sequence gap: Fungal DNA barcoding at Kew”
All UK hypogeous, puffballs, earthstars, waxcaps and tooth fungi.
Two specimens per species from different UK counties.
ITS for 516 specimens.
Manual vs. robotic purification vs. robotic extraction+purification.
2005 seed grant from The Royal Society.
“known fungi which are not yet in the ITS database”
no data
match
identified
sequences
match
unidentified
sequences
Hygrocybe
spp.
others
Geastrum
spp.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
species list entry
not in GenBank
HerbTrack
<30yrs old
And about 100k specimens to go…
sampling
DNA extraction
+ purification
PCR
DNA sequencing
[email protected]
BLAST + comparison
to conspecific
GenBank