Abstract
BackgroundThe marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. However, the lack of genome and transcriptome reference has largely restricted the use of O. melastigma in the assessment of in vivo molecular responses to environmental stresses and the analysis of biological toxicity in the marine environment. Although O. melastigma is believed to be phylogenetically closely related to Oryzias latipes, the divergence between these two species is still largely unknown. Using Illumina high-throughput RNA sequencing followed by de novo assembly and comprehensive gene annotation, we provided transcriptomic resources for the brain, liver, ovary and testis of O. melastigma. We also investigated the possible extent of divergence between O. melastigma and O. latipes at the transcriptome level.ResultsMore than 14,000 transcripts across brain, liver, ovary and testis in marine medaka were annotated, of which 5880 transcripts were orthologous between O. melastigma and O. latipes. Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue. Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma.ConclusionsOrthologous transcripts between O. melastigma and O. latipes, tissue-enriched genes and O. melastigma-enriched transcripts were identified. Genome-wide expression studies of marine medaka require an assembled transcriptome, and this sequencing effort has generated a valuable resource of coding DNA for a non-model species. This transcriptome resource will aid future studies assessing in vivo molecular responses to environmental stresses and those analyzing biological toxicity in the marine environment.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1325-7) contains supplementary material, which is available to authorized users.
Highlights
The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies
Comparison between the transcriptome of freshwater and marine medaka In order to estimate the divergence of the O. melastigma and O. latipes transcriptomes, we first assessed their average nucleotide identities at the transcript level
To aid in the comparison of gene expression among different O. melastigma tissues, we explored two approaches to generate a single consensus transcriptome assembly; (1) Reads-combined Assembly: sequence reads for all tissues were combined prior to being subjected to de novo assembly [23] and (2) Contigs-clustered Assembly: assembly was performed individually for each library
Summary
The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies. There is a trend of using small marine fish as models to study the biological impact of environmental pollutants and stresses on marine organisms, which is an important area of ecotoxicological studies [1] Freshwater fish models, such as zebrafish (Danio rerio) and rainbow trout (Oncorhynchus mykiss), have been widely used for ecotoxicological studies in the freshwater environment. Their responses to environmental toxins can be completely different in marine fish [2,3,4]. The use of O. melastigma as a model in the assessment of in vivo molecular responses to environmental stresses and for analyzing biological toxicity in the marine environment is largely restricted by the lack of molecular resources for O. melastigma [13]
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