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

Abstract

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. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KeGG database 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. 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.

Marine Pollution and Advances in Biomonitoring in Cartagena Bay in the Colombian Caribbean

“…The species Mugil incilis has been studied according to its condition factor to compare different sites [ 163 ], and together with 17 other species, were associated with total mercury content, finding a correlation with their morphometric index [ 59 ]. In addition, the species M. incilis was used as a model for molecular biomarkers of gene expression obtained via the RNAseq technique [ 58 ]. Table 7 summarizes species, biomarkers, and effects reported in Cartagena Bay as an application of the biomonitoring approach for specific pollutants or comparison of the general conditions of different areas.…”

“…Several species have characteristics that allow them to detect the impact of disturbances in the marine environment, presenting effects at the molecular, biochemical, histological, physiological, and morphological levels [ 37 ] and even at community and ecosystem structure levels [ 38 , 39 ]. Therefore, strategies for the assessment of coastal pollution include two approaches: the monitoring of substances in sediment, water, and suspended material and the use of sentinel organisms, such as macroinvertebrates [ 40 , 41 ], foraminifers [ 42 ], algae [ 43 , 44 ], polychaetas [ 45 ], ascidians [ 46 ], echinoderms [ 47 , 48 ], bivalves [ 49 , 50 , 51 , 52 ], crustaceans [ 53 , 54 , 55 , 56 ], and fish [ 57 , 58 , 59 ], among others sensitive to environmental changes.…”