If there were several transcripts for one gene, we took the most 5' annotated transcriptional start site and the most 3' annotated transcriptional termination site to construct the longest possible transcript.
Overall, the most abundant annotated transcript was NADH dehydrogenase subunit 4, which comprised 1190 reads (0.7% of total reads) (Fig. 1).
Following Blast2GO annotation we identified the top 10 most abundant annotated transcripts within the reproductive and non-reproductive SE.
In the mantle, NADH dehydrogenase subunit 4 homologues constituted 5 of the top 10 most abundant annotated transcripts.
In the foot, 5 of the top 10 most abundant annotated transcripts were homologues of foot proteins identified from M. californianus and M. galloprovincialis datasets, specifically adhesive plaque matrix proteins, which constituted 477 reads (1.5% of total).
Finally, 41 An. albimanus transcripts were annotated as Protein of Unknown Function DUF227 (IPR004119), which ranked among the top 20 most abundant annotated transcripts, whereas in An. gambiae this classification was ranked in the 69th place with 43 annotated proteins.
Our analysis revealed that, apart from house-keeping genes, most abundant annotated transcripts were directly related to adaptation to the challenging physico-chemical conditions encountered by A. pompejana, in particular hypoxia, oxidative stress and heavy metals.
Booijink et al. recently showed, using cDNA-AFLP analysis, that most of the annotated transcripts of two fecal samples were included in carbohydrate metabolism [39].
Most of the annotated transcripts likely have a different function, among which the genes were identified only in angiosperms to be involved in the biosynthetic pathway [ 70].
Most of the annotated transcripts corresponded to Picea genes-25.4-39.7%, whereas a smaller percentage, matched Pinus genes, 1.8-12.8%, probably a consequence of more public genomic information available for Picea than for Pinus.
