A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes.
Whole-genome transcriptome profiling is revealing how biological systems are regulated at the transcriptional level. This study reports the development of a robust method to profile and compare the transcriptomes of two nonmodel plant species, Thlaspi caerulescens, a zinc (Zn) hyperaccumulator, and Thlaspi arvense, a nonhyperaccumulator, using Affymetrix Arabidopsis thaliana ATH1-121501 GeneChip arrays (Affymetrix, Santa Clara, CA, USA). Transcript abundance was quantified in the shoots of agar- and compost-grown plants of both species. Analyses were optimized using a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of Thlaspi gDNA with corresponding A. thaliana probes. In silico alignments of GeneChip probes with Thlaspi gene sequences, and quantitative real-time PCR, confirmed the validity of this approach. Approximately 5000 genes were differentially expressed in the shoots of T. caerulescens compared with T. arvense, including genes involved in Zn transport and compartmentalization. Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation.
Hammond
John P
JP
Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK.
Bowen
Helen C
HC
White
Philip J
PJ
Mills
Victoria
V
Pyke
Kevin A
KA
Baker
Alan J M
AJ
Whiting
Steven N
SN
May
Sean T
ST
Broadley
Martin R
MR
D000483:Alleles; D001483:Base Sequence; D001692:Biological Transport; D015342:DNA Probes; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D018745:Genome, Plant; D006706:Homeostasis; D009693:Nucleic Acid Hybridization / Q000379:methods; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000378:metabolism*; D016415:Sequence Alignment; D031227:Thlaspi / Q000235:genetics* / Q000378:metabolism; D015032:Zinc / Q000378:metabolism
D015342:DNA Probes; D010940:Plant Proteins; D012333:RNA, Messenger; D015032:Zinc