The Plant Cell 23: 2045-2063 (2011)

A Guideline to Family-wide Comparative State-of-the-art qRT-PCR Analysis Exemplified with a Brassicaceae Cross-species Seed Germination Case Study  [W][OA]

Kai Graeber*, Ada Linkies*, Andrew T.A. Wood, Gerhard Leubner-Metzger
Both authors contributed equally to this work
University of Freiburg, Faculty of Biology, Institute for Biology II, Botany / Plant Physiology, D-79104 Freiburg, Germany, Web: 'The Seed Biology Place' (K.G., A.L., G.L.-M.)
The University of Nottingham, Division of Statistics, School of Mathematical Sciences, University Park, Nottingham NG7 2RD, United Kingdom (A.T.A.W.)

Received February 8, 2011; revised May 6, 2011; accepted May 27, 2011; published June 10, 2011.

Supplemental Table 1. Sequence similarities to Arabidopsis and accession numbers of Lepidium sativum FR14 reference gene cDNA sequences.

Lepidium sativum reference genes
cDNA sequence name
GenBank accession numbers AGI code of putative
Arabidopsis ortholog
e-value % sequence similarity between the two species
LesaG17210 HQ912755 At1G17210 0 92
LesaG04660 HQ912754 At2G04660 0 92
LesaG19980 HQ912756 At2G19980 1e-71 77
LesaG20000 HQ912757 At2G20000 4e-160 92
LesaG04320 HQ912753 At4G04320 8e-90 91
LesaCYP1 HS981851 At4G38740 7e-42 94
LesaACT7 HS981849 At5G09810 8e-32 100
LesaACT8 HS981850 At1G49240 8e-33 96
LesaEF1-α HS981853 At5G60390 6e-20 94
LesaCYP5 HS981852 At2G29960 9e-33 93
LesaUBQ11 HS981854 At4G05050 2e-34 92

Synopsis: Developmental processes like seed germination are characterised by massive transcriptome changes. This study compares seed transcriptome datasets of different Brassicaceae to identify stable expressed reference genes for cross-species qRT-PCR normalisation. A workflow is presented for improving RNA quality, qRT-PCR performance, and normalisation when analysing expression changes across species.
Article in PDF format (1.2 MB)
Supplemental  data file (156 KB)
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Hyperlink to
Datasets 1 to 3
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