“Molecular mechanisms of speciation in Aquilegia & Pachycladon ”
T ranscriptome and p roteome studies of New Zealand alpine Pachycladon
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Transcript of T ranscriptome and p roteome studies of New Zealand alpine Pachycladon
Transcriptome and proteome studies of New Zealand alpine Pachycladon
NZPRN 2009
Claudia Voelckel, Mehdi Mirzaei, Michael Reichelt, Luke Luo, Dana Pascovici, Peter B Heenan, Sylvia S Schmidt, Bart Janssen, Paul A Haynes, Peter J Lockhart
Q: Adaptive diversification? Q: Mediated by which genes?
A: Comparative gene expression profiling in common gardens
FA
ST
EN
EN
LA
CHEX
NZ
WA
Questions & Approach
P. cheesemanii (CH)
P. exile (EX)
P. novae-zelandiae(NZ)
CHEX
NZ
Pachycladon super net work, S. Joly, unpubl.
LincolnPlant growth
Peter Heenan Murray Dawson
AucklandMicroarray analysis
Bart Janssen Luke Luo Silvia Schmidt
Jena Glucosinolate
analysis
Michael Reichelt
PalmyLink all data
Claudia VoelckelPete Lockhart
SydneyProtein analysis
Paul A. Haynes Mehdi Mirzai Dana Pascovici
People who helped:
almost submitted
1. Protein profiling as a validation of transcript profiling? How much overlap?
Specific questions:
3. To what extend will transcript and protein profiling make different predictions regarding downstream physiological differences?
4. Will phylogenetic relationships be reflected in transcript, protein and metabolite profiles?
2. Can we predict physiological differences between CH, EX and NZ and what are they?
CH
EX+NZ EX NZ
T 371 69 936
P 124 60 141
EX
CH+NZ CH NZ
T 134 45 946
P 109 161 110
NZ
CH+EX CH EX
T 305 221 297
P 321 359 211
9601 loci
1489 loci
Results
8527 4151074
T PTP
CH EX NZ
CH 0.52 0.43 0.30
EX 0.47 0.45 0.32
NZ 0.40 0.36 0.34
TP
Overall correlation: Specifically up-regulated genes:
T = transcript profiling, P = protein profiling
97 6129*T PTP
EX+NZ
23%32%
CH
18 814
14 2288
T PTP
T PTP
CH+NZ
CH+EX
18%4%
36%3%
220 4456 *
183 6327 *
13 1439 *
T PTP
T PTP
T PTP
NZ
NZ
EX
20%56%
13%30%
40%6%
20 414 *
5 1251
11 2479 *
T PTP
T PTP
T PTP
EX
CH
CH
16%9%
16%<1%
45%4%
EX
NZ
Specific Genes Found by T AND P
Interconversion of carbon dioxide and bicarbonate (carbonic anhydrase)
Interconversion of carbon dioxide and bicarbonate (carbonic anhydrase)
Draught response
Draught response
Serine racemase
Vegetative storage proteins
97 6129*
18 814
14 2288
T PTP
T PTP
T PTP
EX+NZ
CH+NZ
CH+EX
23%32%
18%4%
36%3%
CH
EX
NZ
Specific Genes Found by T AND P
T EX+NZ EX NZ
CH AL up AL up AL upC4 up
CH+NZ CH NZ
EX - - -
CH+EX CH EX
NZ - - -
P EX+NZ EX NZ
CH - C4 up -
CH+NZ CH NZ
EX - - -
CH+EX CH EX
NZ C4 up C4 up C4 up
Predictions from T and P: Glucosinolate Biosynthesis
CH EX NZ CH EX NZ
EX+NZ EX NZ
CH - - -
CH+NZ CH NZ
EX iso ? iso?
CH+EX CH EX
NZ ? ? -
EX+NZ EX NZ
CH - - -
CH+NZ CH NZ
EX ? - -
CH+EX CH EX
NZ nitriles??
nitriles??
nitriles??
Predictions from T and P: Glucosinolate Hydrolysis
P. cheesemaniiP. novae-zelandiae
T CH EX NZ
CH 1 0.91 0.74
EX 1 0.83
NZ 1
P CH EX NZ
CH 1 0.75 0.59
EX 1 0.72
NZ 1
= =
Profiling Patterns Through the Phylogenetic Lens:
3MSO
P4M
SOB
3-Bu
teny
l4M
TB8M
SOO
6MSO
H
4OH
I3M
7MTH
1MO
I3M
4MO
I3M
7MSO
H
3MTP
S-2O
H3-
But.
Ally
l
EX
CH*
NZ*
CHEX
NZ≠
Glucosinolates
1. Protein profiling as a validation of transcript profiling? How much overlap? – overlap small but significant
Some Answers:
3. To what extend will transcript and protein profiling make different predictions regarding downstream physiological differences?glucosinolate phenotypes better predicted by protein profiling
4. Will phylogenetic relationships be reflected in transcript, protein and metabolite profiles? – not in metabolite profiles, selection?
2. Can we predict physiological differences between CH, EX and NZ and what are they? – yes (C02 enzymes, draught response, glucosinolate metabolism)
Thanks to:
YOU!
FundingMarsden & Humboldt Foundation
New ZealandLandcare: Peter Heenan, Murray Dawson, Kat Trought
Plant and Food: Bart Janssen, Luke Luo, Silvia SchmidtAWC: Pete Lockhart, Christine Reinsch, Hanna Daniel
GermanyMPICE: Michael Reichelt, Jonathan Gershenzon
AustraliaMacquarie University: Mehdi Mirzai, Dana Pascovici, Paul Haynes, Mark Westoby