Complementary DNA preparations were prepared for sequencing using the Roche Library Preparation Kit (http://www.roche.com/ ), Roche Emulsion PCR kit and PicoTiterPlates. Sequencing of B. napus was performed with the Roche GS FLX Titanium and for other species with Roche GS FLX.
Reads were trimmed to remove low-quality and primer sequences using Seq-Clean and assembled with CAP3 (Huang and Madan, 1999 (link)). Initially, 5% of the data were assembled to identify and remove abundant ESTs from the full dataset using BLAT (Kent, 2002 (link)). The reduced dataset then underwent two rounds of assembly with CAP3. First-round CAP3 parameter settings for percentage match, overlap length, maximum over-hang percentage, gap penalty, and base quality cut-off for clipping were p90, o50, h15, g2, and c17, respectively. For the second round, overlap length was changed to 100. The resultant contigs were annotated with a translated BLAST against the TAIR8 database (E-value cut-off 10−10) and further annotated based on information athttp://aralip.plantbiology.msu.edu/ . The number of ESTs/100 000 ESTs was used as a measure for gene expression. The EST levels and annotations for the oilseed orthologs of >350 Arabidopsis proteins related to lipid and carbohydrate metabolism are provided in Table S1a and S1b. The DNA sequences from this study are deposited at the GenBank Short Read Archive (SRA) with accession numbers provided in Table S4 . The EST level data for all orthologs of Arabidopsis proteins (>10 ESTs) are provided in Table S5 . Contig nucleotide sequences for R. communis, B. napus and E. alatus are provided as fasta files (RcContigSeq, BnContigSeq and EaContigSeq, respectively).
We used SOMs to evaluate temporal EST expression patterns of 228 proteins related to lipid and carbohydrate metabolism. Expression data were centered and normalized for each protein using adjust methods in Cluster 3.0 (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm ) and SOM clusters were generated using Gene Cluster 2.0 (http://www.broadinstitute.org/cancer/software/genecluster2/gc2.html ).
Reads were trimmed to remove low-quality and primer sequences using Seq-Clean and assembled with CAP3 (Huang and Madan, 1999 (link)). Initially, 5% of the data were assembled to identify and remove abundant ESTs from the full dataset using BLAT (Kent, 2002 (link)). The reduced dataset then underwent two rounds of assembly with CAP3. First-round CAP3 parameter settings for percentage match, overlap length, maximum over-hang percentage, gap penalty, and base quality cut-off for clipping were p90, o50, h15, g2, and c17, respectively. For the second round, overlap length was changed to 100. The resultant contigs were annotated with a translated BLAST against the TAIR8 database (E-value cut-off 10−10) and further annotated based on information at
We used SOMs to evaluate temporal EST expression patterns of 228 proteins related to lipid and carbohydrate metabolism. Expression data were centered and normalized for each protein using adjust methods in Cluster 3.0 (
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