454 pyrosequencing based whole transcriptome analysis of the poultry red mite Dermanyssus gallinae
Background The poultry red mite Dermanyssus gallinae (De Geer, 1778) is a serious problem in poultry farming causing substantial economic losses every year. Although this mite is the most important ectoparasite in poultry farming, nucleotide data are rare in the public databases. Therefore, de novo sequencing covering the transcriptome of D. gallinae was carried out. Results The obtained ~1.5 million 454 pyrosequencing reads were clustered and assembled to 232,097 singletons and 42,130 contiguous sequences (contigs) which were subsequently clustered into 24,140 isogroups consisting of 35,788 isotigs. Sequences possibly originating from undesired contaminating organisms like those of bacteria and the host Gallus gallus (Linnaeus, 1758), were identified and subtracted from the data sets. In total 267,471 sequences (231,663 singletons, 56 contigs and 35,752 isotigs) remained for further analyses. Of these, 11.2% showed sequence homology to proteins derived from other organisms. To gain functional knowledge about identified D. gallinae proteins, sequences were assigned to Gene Ontology (GO) terms resulting in 15,482 annotated sequences (8,034 singletons, 18 contigs and 7,430 isotigs). GO mapping underlined biological characteristics on the genetic level in terms of response to environmental stimuli, development and growth. Additionally, GO annotation suggested vector competence of the poultry red mite for the avian leukosis virus. Furthermore, D. gallinae sequences were mapped to 127 pathway maps and analyzed for functional protein domains. Conclusions De novo 454 pyrosequencing of the poultry red mite has made a large transcriptome dataset available. It provides new insights in general mite genetics and helps to understand the biology of the parasitic mite D. gallinae. Furthermore, it lays a foundation for future studies on stage-specific transcriptomics as well as genomic, proteomic, and metabolomic explorations and might provide new perspectives to control this parasitic mite by identifying possible drug targets or vaccine candidates.