Tench (Tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles

Tench, Tinca tinca is a freshwater species which receives increasing attention as marine resources are overexploited and alternative feed components must be implemented to enable sustainable development of aquaculture. The aim of the study was to provide scientists and fish farmers with first high quality annotated tench transcriptome and open a new chapter in tench research, especially when practical diets are tested. Therefore, the second aim was to identify differentially expressed contigs (DECs) in tench gut after 86-day trial where adult tench females were fed with 0% and 100% replacement of fish meal (FM) with poultry by-product meal (PBM). De novo assembling using de novo RNA-Seq Assembly Pipeline (DRAP) produced 64070 contigs where these exceeding 1 kbp were mostly annotated. Microsatellite search identified 23668 SSRs and SNPs were distributed in 118002 transitions and 83577 transversions. High quality of the assembly and annotation completeness of the tench transcriptome was confirmed using BUSCO and by mapping contigs against common carp, Cyprinus carpio and zebrafish, Danio rerio data sets. Analysis of gene expression differences between gut samples tench fed with FM and PBM diets revealed 721 and 69 DECs using edgeR and DESeq2, respectively. Venn diagram for these results filtered out 57 DECs which were common for both analysis. Due to a low number of annotated DECs enrichment analysis provided a low number of useful contigs for pathway or functional analysis. Nevertheless, each contig in the set was analysed through BLASTn and BLASTx and eighteen DECs were characterised and identified as mainly involved in response to different immune stimuli and disease states (e.g. cluster of differentiation 48, F-type lectin), cell adhesion (e.g. paracingulin), digestion (e.g. serine proteases) and signal transduction (e.g. neurexophilin 3, complexin 2). Moreover, study has shown that most of the identified in our study DECs (70.2%) were down regulated in gut samples of tench fed with PBM comparing to these with FM-based feed. This observation might indicate on disorganization of inter-epithelial junctions in ongoing inflammation process. Our de novo tench gut transcriptome assembly (online NGS Pipeline) provide a guide for further diverse studies because, understanding feed-gut interactions and intestinal homeostasis in farmed tench is important to maximise performance of this species and to ensure that freshwater aquaculture continues to be a sustainable source of food for a growing world population.