Abstract
The new technologies for next-generation sequencing (NGS) and global gene expression analyses that are widely used in molecular medicine are increasingly applied to the field of fish biology. This has facilitated new directions to address research areas that could not be previously considered due to the lack of molecular information for ecologically relevant species. Over the past decade, the cost of NGS has decreased significantly, making it possible to use non-model fish species to investigate emerging environmental issues. NGS technologies have permitted researchers to obtain large amounts of raw data in short periods of time. There have also been significant improvements in bioinformatics to assemble the sequences and annotate the genes, thus facilitating the management of these large datasets.The combination of DNA sequencing and bioinformatics has improved our abilities to design custom microarrays and study the genome and transcriptome of a wide variety of organisms. Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods. These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.
Highlights
Research in fish physiology, genetics, evolution, immunology, and endocrinology using non-model species has seen a marked increase in the utilization of genomic information over the last decade
This review describes the latest next-generation sequencing (NGS) platforms available and bioinformatics tools that can be employed to examine the transcriptome of non-model fish species
While next-generation sequencers are reviewed for general purposes elsewhere (e.g., Mardis, 2008), we provide a brief description of the various technologies followed by a discussion of the relative advantages of each platform for fish toxicogenomics research
Summary
Genetics, evolution, immunology, and endocrinology using non-model species has seen a marked increase in the utilization of genomic information over the last decade. Gene expression profiling using techniques such as microarrays plays a key role for biomarkers characterization and discovery of toxicity pathways (Denslow et al, 2007; Ju et al, 2007). Research in this field often requires the analysis of complex genomic events using extensive time course and dose response studies in multiple tissues of teleost fish, which can be difficult due to logistics and cost. Studies that have utilized NGS technologies using fish species are reviewed www.frontiersin.org
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