A de novo Transcriptome Assembly of the European Flounder (Platichthys flesus): The Preselection of Transcripts Encoding Active Forms of Enzymes

The RNA sequencing data sets available for different fish species show a potentially high variety of forms of enzymes just in teleosts. This is primarily considered an effect of the first round of whole-genome duplication with mutations in duplicated genes (isozymes) and alternative splicing of mRNA (isoforms). However, the abundance of the mRNA transcript variants is not necessarily reflected in the abundance of active forms of proteins. We have investigated the transcriptional profiles of two enzymes, aralkylamine N-acetyltransferase (AANAT: EC 2.3.1.87) and N-acetylserotonin O-methyltransferase (ASMT: EC 2.1.1.4), in the eyeball, brain, intestines, spleen, heart, liver, head kidney, gonads, and skin of the European flounder (Platichthys flesus). High-throughput next-generation sequencing technology NovaSeq6000 was used to generate 500M sequencing reads. These were then assembled and filtered producing 75k reliable contigs. Gene ontology (GO) terms were assigned to the majority of annotated contigs/unigenes based on the results of PFAM, PANTHER, UniProt, and InterPro protein database searches. BUSCOs statistics for metazoa, vertebrata, and actinopterygii databases showed that the reported transcriptome represents a high level of completeness. In this article, we show how to preselect transcripts encoding the active enzymes (isozymes or isoforms), using AANAT and ASMT in the European flounder as the examples. The data can be used as a tool to design the experiments as well as a basis for discussion of diversity of enzyme forms and their physiological relevance in teleosts.

Automated summary

Research shows that the diversity of enzyme forms in teleosts is mainly influenced by whole-genome duplication and selective mRNA splicing. By analyzing the transcriptional profiles of the European flounder in different tissues, we demonstrate how to preselect transcripts encoding active enzymes and find that the reported transcriptome is highly complete.