Finally, analysis of the PtGS2 duplicate revealed that the transcripts of this family member were the most abundant in the young leaves (A1), and decreased progressively from the top to the bottom of the tree, with the lowest values detected in the roots.
In the case of duplicated genes, parts of the transcripts were highly similar and merged into the same contig, but reads covering the regions of the duplicated genes that have diverged were split into different contigs (nodes).
Interestingly, the highest levels of the transcripts for PtGS1.1 duplicates were also observed in the leaf lamina, with decreased levels observed in the parenchyma cells.
Transcriptome reconstruction was performed using uniquely mapped reads or, alternatively, all the reads (unique and repeated) in order to improve the identification of the transcripts that are duplicated in the P. profundum genome like for example the CRISP elements and to better define the transcript structure of the genes having repeated regions.
All real-time PCR reactions were done in duplicate and the transcript levels were normalized against those of β-actin.
Each cDNA was diluted and run in duplicate, and the transcript copy number was expressed per nanogram of total RNA.
Doreh appears in eight of the transcripts.
Make a duplicate of the background layer.
Each sample was run in duplicates and the transcript quantity was normalized to the mRNA level of cyclophilin A (Applied Biosystems, Foster City, CA).
To compare the gene profiles of the different treatments and to determine the number of transcripts regulated by each treatment, we eliminated duplicates of transcripts represented more than once as well as transcripts with unknown gene identification numbers.
A 3-fold difference in the median number of duplicate reads between AS and SMS across all transcripts observed in all samples was maintained across the majority of the transcript length (Figure 2D).
