Overall, transcriptome sequencing from the prefrontal cortex of two fox individuals identified over 30,000 high-confidence fox-specific SNPs, fox orthologs of over 14,000 dog genes, and yielded new insights into potentially important differences in expression of genes in the pre-frontal cortex between tame and aggressive foxes.
Overall, transcriptome sequencing detected 21,743 genes with at least one read (72.5% of predicted gene models) and 13,503 genes (45% of predicted gene models) were confidently detected above the cutoff threshold of 64 reads in at least one of the stages profiled.
These reads had a mean length of 278 bp, and an overall length distribution characteristic of 454 transcriptome sequencing with Titanium chemistry on this platform (Figure 2).
Nonetheless, the large number of singleton sequences with BLAST matches (Table 11) indicates that unassembled sequences still provide an abundance of valuable sequence information and improve overall transcriptome coverage breadth.
The quality of the assembled transcriptome was critically assessed according to the guideline provided by Gibson et al. [ 14] by evaluating sequence quality, assembly quality, overall transcriptome completeness, and transcriptional activity.
Overall the data obtained by qRT-PCR were highly consistent with the transcriptome sequencing data.
In terms of overall transcriptome size, the 42,620 contigs of P. borchgrevinki are comparable to several recently sequenced teleost transcriptomes, namely, 54,921contigs from the guppy Poecilia reticulata transcriptome [ 26], 36,110 contigs from the European eelpout Zoarces viviparus[ 27], and 42,953 contigs from the Pacific herring Clupea pallasii transcriptome [ 28].
The overall sequencing yield of this study (~15,000 MB) exceeded that of all but two published cnidarian transcriptome sequencing projects.
Overall, we obtained expression evidence for 1,401 of 1,427 ORF models with assigned enzymatic functions based on targeted transcriptome sequencing results and sequencing of the clones, though clearly not all of these ORF models can be considered verified.
For studies involving different donors, whole genome and transcriptome sequencing would be required for each donor and their tissues, significantly adding to the overall cost and labor requirements.
Overall, these comparisons with previous studies highlight the potential for our method to improve sequencing depth and efficiency in future transcriptome sequencing efforts.
