RNA sequencing reveals distinct gene expression patterns during the development of parasitic larval stages of the salmon louse (Lepeophtheirus salmonis).

The salmon louse (Lepeophtheirus salmonis), an ectoparasitic copepod on salmonids, has become a major threat for the aquaculture industry. In search for new drugs and vaccines, transcriptome analysis is increasingly used to find differently regulated genes and pathways in response to treatment. However, the underlying gene expression changes going along with developmental processes could confound such analyses. The life cycle of L. salmonis consists of eight stages divided by moults. The developmental rate of salmon lice on the host is not uniform. Individual- and sex-related differences are found leading to individuals of unlike developmental status at same sampling time point after infection. In this study, we analyse L. salmonis from a time series by RNA sequencing applying a method of separating individuals of different instar age independent of sampling time point. Lice of four stages divided into up to four age groups within the stage were analysed in triplicate (total of 66 samples). Gene expression analysis shows that the method for sorting individuals was successful. Many genes show cyclic expression patterns over the moulting cycles. Overall gene expression differs more between lice of different age within the same stage than between lice of different stage but same instar age.

BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.

The growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. In this paper, we describe the current state and latest developments of our BRIGEP bioinformatics software system consisting of three web-based applications: GenDB, EMMA and ProDB. These applications facilitate the processing and analysis of bacterial genome, transcriptome and proteome data and are actively used by numerous international groups. We are currently in the process of extensively interconnecting these applications. BRIGEP was developed in the Bioinformatics Resource Facility of the Center for Biotechnology at Bielefeld University and is freely available. A demo project with sample data and access to all three tools is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/. Code bundles for these and other tools developed in our group are accessible on our FTP server at ftp.cebitec.uni-bielefeld.de/pub/software/.