Transcriptome sequencing of maraena whitefish (Coregonus maraena)

Andreas Brietzke,Andreas Borchel,Simone Altmann,Mareen Nipkow,Alexander Rebl,Ronald M Brunner,Tom Goldammer

doi:10.1016/j.margen.2016.05.006

Andreas Brietzke, Andreas Borchel + Show 5 more

Open Access

https://doi.org/10.1016/j.margen.2016.05.006

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Abstract

Maraena whitefish (Coregonus maraena, Bloch, 1779) is a high-quality food fish belonging to the family Salmonidae with considerable economic relevance in the Baltic area. Aquaculture of this species is fundamental for its successful conservation and thus sustainable fisheries. Robust fishes obtained from breeding lines build the basis for effective aquaculture. Doubtless, the utilization of transcriptome sequencing and identification of genetic markers contribute to this aim. 454 FLX Titanium Sequencing provided 1.31 million sequence reads representing a first insight into the C. maraena transcriptome. The 454 Newbler Assembly arranged 29,094 contigs with an average length of 798bp. We found a whole series of transcripts highly probably resulting from ancient genome duplication and annotated 2887 different transcripts with an average length of 812bp. Functional annotation obtained a transcript composition predominantly comprising enzyme-coding genes.

Highlights

Maraena whitefish (Coregonus maraena) is a white-fleshed food fish in the riparian states of the Baltic Sea, which is in neither flavor nor nutrition inferior to its famous salmonid relatives, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss)
A combination of extensive fishing, eutrophication of its estuary spawning areas, and habitat fragmentation through anthropic obstruction have brought the population of C. maraena to the edge of extinction, especially in the southern Baltic Sea area (Olsson et al, 2012)
To relieve the native population and guarantee a continuous supply of whitefish as an interregional delicacy, farming of C. maraena was successfully launched in Mecklenburg-Western Pomerania, Germany (Arndt and Jansen, 2008)

Summary

Introduction

Maraena whitefish (Coregonus maraena) is a white-fleshed food fish in the riparian states of the Baltic Sea, which is in neither flavor nor nutrition inferior to its famous salmonid relatives, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). A combination of extensive fishing, eutrophication of its estuary spawning areas, and habitat fragmentation through anthropic obstruction have brought the population of C. maraena to the edge of extinction, especially in the southern Baltic Sea area (Olsson et al, 2012). To relieve the native population and guarantee a continuous supply of whitefish as an interregional delicacy, farming of C. maraena was successfully launched in Mecklenburg-Western Pomerania, Germany (Arndt and Jansen, 2008). The establishment of C. maraena breeding lines has encountered aquaculture-related challenges such as slow growth rates or susceptibility towards husbandry stress and pathogens (Altmann et al, 2015). Marker-assisted breeding strategies require profound knowledge of the genetic constitution of C. maraena, but only few relevant sequences are publicly available to Abbreviations: CKMT2, creatine kinase, mitochondrial 2; HNRPDL, heterogeneous nuclear ribonucleoprotein D like; TGFBI, transforming growth factor beta induced; TUBA1C, tubulin alpha 1c. We sequenced the transcriptome of C. maraena across tissues and ages as a starting point for future investigations

Sample collection and sequencing

Transcriptome assembly

Functional annotation

Data deposition