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