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The most abundant transcript uniquely expressed in LD has only 558 reads (PGSC0003DMG400026590) whereas the most abundant unique transcript under SD conditions has only 208 reads (PGSC0003DMG400016462).
The extra 80% assembled contigs in the normalized cDNA pools suggests that normalization played a critical role in enriching low-abundant unique transcripts and increasing the total number of cDNAs.
Strongly differentiated genes (>4 fold change and FDR ≤ 0.05; Figure 2b) were highly abundant in the desert strain (824 unique transcripts; Additional file 1: Table S1) relative to the other two strains (montane = 58; Additional file 2: Table S2; F1 = 192; Additional file 3: Table S3), particularly in upregulated transcripts.
Normalization of the cDNA greatly reduces the frequency of abundant transcripts, and increases the rate recovery of unique transcripts [ 10].
The most abundant class, both in terms of the number unique transcripts and total ESTs, was classified as protein synthesis machinery which contains 32 concensus sequences and 67 singletons totaling 655 ESTs.
Normalization of the cDNA has been reported to be especially important in gene discovery when the cDNA used for sequencing is pooled from many tissues or individuals [ 39- 41], and to considerably reduce the frequency of abundant transcripts thus increasing the possibility to reach also unique transcripts of isoenzymes with low expression levels.
Further, the fraction of unique transcripts recovered is consistent with the fraction previously reported23.
When N transcripts are sequenced, there are s(N) = S[1−P(0|N)] unique transcripts expected to be detected.
Description of the number of unique transcripts and unique probes.
Nonredundant unique transcripts were defined as unigenes.
In total, 16,603 unique transcripts and 102 proteins were identified.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com