De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Abstract

Background Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. Results A total of 32.082.124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93.947 contigs (with N50 = 2.019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (36.6%). Using a sequence similarity search against the public databases GO and KEGG, a total of 71.271 and 16.974 contigs were annotated, respectively. KEGG showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. Conclusions This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.