Molecular phylogeny and evolution of the proteins  encoded by the common vampire bat (Desmodus rotundus) submaxillary gland
Submaxillary gland anterior or posterior lobes of two specimens were dissected out and pooled. Total RNA extracted using the standard TRIzol Plus method (Invitrogen). Extracts were enriched for mRNA using standard RNeasy mRNA mini kit (Qiagen) protocol. mRNA was reverse transcribed, fragmented and ligated to a unique 10-base multiplex identifier (MID) tag prepared using standard protocols and applied to one PicoTitrePlate (PTP) for simultaneous amplification and sequencing on a Roche 454 GS FLX+ Titanium platform (Australian Genome Research Facility). Automated grouping and analysis of sample-specific MID reads informatically separated sequences from the other transcriptomes on the plates, which were then post-processed to remove low quality sequences before de novo assembly into con¬tiguous sequences (contigs) using v 3.4.0.1 of the MIRA software program. Assem¬bled contigs were processed using CLC Main Work Bench (CLC-Bio) and Blast2GO bioinformatic suite to provide Gene Ontology, BLAST and domain/Interpro annotation. The above analyses assisted in the rationalisation of the large numbers of assembled contigs into phylogenetic ‘groups’ for detailed phylogenetic analyses