De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis

Genes

DylanJ. Richards¹  Nisha Agarwal²  E. Starr Hazard³  Gary Hardiman⁴  Ludivine Renaud⁴  John Hyde⁵ 

[1] Bioengineering Department, Clemson University, Charleston, SC 29425, USA;Biomedical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA;Center for Genomic Medicine, Bioinformatics, Medical University of South Carolina, Charleston, SC 29425, USA;Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA 92037, USA;

关键词: sardine;    mackerel;    turbot;    RNA sequencing;    de novo transcriptome assembly;    genomic biomarkers;   

DOI  :  10.3390/genes9110521

来源: DOAJ

【 摘 要 】

The monitoring of marine species as sentinels for ecosystem health has long been a valuable tool worldwide, providing insight into how both anthropogenic pollution and naturally occurring phenomena (i.e., harmful algal blooms) may lead to human and animal dietary concerns. The marine environments contain many contaminants of anthropogenic origin that have sufficient similarities to steroid and thyroid hormones, to potentially disrupt normal endocrine physiology in humans, fish, and other animals. An appropriate understanding of the effects of these endocrine disrupting chemicals (EDCs) on forage fish (e.g., sardine, anchovy, mackerel) can lead to significant insight into how these contaminants may affect local ecosystems in addition to their potential impacts on human health. With advancements in molecular tools (e.g., high-throughput sequencing, HTS), a genomics approach offers a robust toolkit to discover putative genetic biomarkers in fish exposed to these chemicals. However, the lack of available sequence information for non-model species has limited the development of these genomic toolkits. Using HTS and de novo assembly technology, the present study aimed to establish, for the first time for Sardinops sagax (Pacific sardine), Scomber japonicas (Pacific chub mackerel) and Pleuronichthys verticalis (hornyhead turbot), a de novo global transcriptome database of the liver, the primary organ involved in detoxification. The assembled transcriptomes provide a foundation for further downstream validation, comparative genomic analysis and biomarker development for future applications in ecotoxicogenomic studies, as well as environmental evaluation (e.g., climate change) and public health safety (e.g., dietary screening).

【 授权许可】

Unknown