Open Access Research article

Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

Claudia Voelckel1, Mehdi Mirzaei2, Michael Reichelt3, Zhiwei Luo4, Dana Pascovici5, Peter B Heenan6, Silvia Schmidt34, Bart Janssen4, Paul A Haynes2 and Peter J Lockhart1*

Author Affiliations

1 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand

2 Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

3 Max Planck Institute for Chemical Ecology, Jena, Germany

4 Plant and Food Research, Mount Albert, Auckland, New Zealand

5 Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia

6 Landcare Research, Lincoln, New Zealand

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BMC Evolutionary Biology 2010, 10:151  doi:10.1186/1471-2148-10-151

Published: 20 May 2010



Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three Pachycladon species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species.


Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins) and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase), the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases), water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase) and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis). Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not.


We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three Pachycladon species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence.