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Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes.

Lai KP, Li JW, Wang SY, Chiu JM, Tse A, Lau K, Lok S, Au DW, Tse WK, Wong CK, Chan TF, Kong RY, Wu RS - BMC Genomics (2015)

Bottom Line: Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma.Orthologous 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. balllai@hku.hk.

ABSTRACT

Background: The 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.

Results: More 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.

Conclusions: Orthologous 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.

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Workflow of this study. A) Organ-specific transcriptome sequencing using the Illumina GAIIx platform. B) Overview of the procedure to investigate the divergence between marine and freshwater medaka at the transcriptome level. C) Pipeline of de novo transcriptome assembly. Refer to main text for details. D) Comparison of inter-organ transcription and marine-to-freshwater medaka.
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Fig1: Workflow of this study. A) Organ-specific transcriptome sequencing using the Illumina GAIIx platform. B) Overview of the procedure to investigate the divergence between marine and freshwater medaka at the transcriptome level. C) Pipeline of de novo transcriptome assembly. Refer to main text for details. D) Comparison of inter-organ transcription and marine-to-freshwater medaka.

Mentions: Tissue specific transcriptome from of O. melastigma were assembled from high-throughput strand-specific RNA-Seq. The possible divergence between marine and freshwater medaka at the transcriptome level was assessed by comparisons of sequences deposited in public databases and the assemblies generated in this study. A single consensus transcriptome was generated for gene annotation and inter-organ comparative analysis and marine-to-freshwater medaka transcriptome comparison. The overall workflow of the study is shown in FigureĀ 1.Figure 1


Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes.

Lai KP, Li JW, Wang SY, Chiu JM, Tse A, Lau K, Lok S, Au DW, Tse WK, Wong CK, Chan TF, Kong RY, Wu RS - BMC Genomics (2015)

Workflow of this study. A) Organ-specific transcriptome sequencing using the Illumina GAIIx platform. B) Overview of the procedure to investigate the divergence between marine and freshwater medaka at the transcriptome level. C) Pipeline of de novo transcriptome assembly. Refer to main text for details. D) Comparison of inter-organ transcription and marine-to-freshwater medaka.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4352242&req=5

Fig1: Workflow of this study. A) Organ-specific transcriptome sequencing using the Illumina GAIIx platform. B) Overview of the procedure to investigate the divergence between marine and freshwater medaka at the transcriptome level. C) Pipeline of de novo transcriptome assembly. Refer to main text for details. D) Comparison of inter-organ transcription and marine-to-freshwater medaka.
Mentions: Tissue specific transcriptome from of O. melastigma were assembled from high-throughput strand-specific RNA-Seq. The possible divergence between marine and freshwater medaka at the transcriptome level was assessed by comparisons of sequences deposited in public databases and the assemblies generated in this study. A single consensus transcriptome was generated for gene annotation and inter-organ comparative analysis and marine-to-freshwater medaka transcriptome comparison. The overall workflow of the study is shown in FigureĀ 1.Figure 1

Bottom Line: Lastly, the identification of marine medaka-enriched transcripts suggested the necessity of generating transcriptome dataset of O. melastigma.Orthologous 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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China. balllai@hku.hk.

ABSTRACT

Background: The 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.

Results: More 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.

Conclusions: Orthologous 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.

Show MeSH
Related in: MedlinePlus