Duplicate transcripts were removed, and then the coordinates based on Galgal4 assembly were obtained for the transcript IDs.
We used custom scripts to ensure that every CDS range had a corresponding exon range and to remove duplicate transcripts.
This 715-transcript dataset contained 48 duplicate transcripts, yielding 667 unique transcripts which correspond to 437 unique genes for subsequent GOMiner analyses.
This list was obtained by comparing profiles of genes detected by the three treatments, excluding duplicate transcripts, unknown transcripts and transcripts not detected in one or two of the treatments.
We filter out duplicate transcripts (transcripts sharing exonic coordinates and thus differing only in the locations of their untranslated regions) and alternative haplotype/supercontig entries from the cDNA sequences and the genome assembly.
Retained duplicate transcripts corresponding to isoflavone synthase/cellulose synthase, galactinol synthase, raffinose synthase and caffeoyl-CoA o-methyltransferase were identified with TBLASTX (default parameters) using a reference sequence against all soybean ESTs [ 58].
The 11 additional sequenced BACs were anchored by either RFLP clones (A711; UMb001-24d13 and Umb001-5f5) or by the duplicate transcripts cellulose synthase (gmw2-133d1 and gmw1-93l19), galactinol synthase gmw1-5g166 and gmw1-103e11), raffinosynthasease (gmw1-13o17 and gmw1-8g7) and caffeoyl-CoA O-methyltransferase gmw1-58k33, gmw1-57d24 and gmw1-27d20).
Most of these duplicated transcripts are located in the vicinity of transposases that exist in multiple copies in the genome of strain N315.
We also used MEGA3 to determine the evolution of the recently duplicated transcripts.
Although output transcripts are clustered and duplicated transcripts are removed, many duplicates are difficult to detect and errors can accumulate in the cluster-remove step.
The large number of duplicated transcripts observed in the Atlantic salmon genome is consistent with the hypothesis of an ancestral salmonid genome duplication, though it is surprising that so many of the duplicated contigs are so similar.
