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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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Global comparison of annotated genes in the brain, liver, ovary and testis of marine medaka. Of the identified genes, 2692 were brain-enriched. 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. 6821 annotated genes were common to all tissues in both males and females.
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Fig3: Global comparison of annotated genes in the brain, liver, ovary and testis of marine medaka. Of the identified genes, 2692 were brain-enriched. 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. 6821 annotated genes were common to all tissues in both males and females.

Mentions: Global comparison of annotated genes showed that 7157 (34.5%) genes that were annotated in only a single tissue. We found 2692 brain-enriched genes, while 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. Furthermore, 6821 annotated genes were common to all tissues in both males and females (Figure 3). The gonad-enriched genes were enriched in the following GO terms: sexual reproduction and gamete generation. The brain-enriched genes were enriched in functions related to channel activity, synaptic transmission and cell-cell adhesion. The liver-enriched genes were enriched in functions related to metabolic processes, transferase and mannosidase activity (Table 2, Additional file 10: Table S10).Figure 3


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)

Global comparison of annotated genes in the brain, liver, ovary and testis of marine medaka. Of the identified genes, 2692 were brain-enriched. 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. 6821 annotated genes were common to all tissues in both males and females.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Global comparison of annotated genes in the brain, liver, ovary and testis of marine medaka. Of the identified genes, 2692 were brain-enriched. 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. 6821 annotated genes were common to all tissues in both males and females.
Mentions: Global comparison of annotated genes showed that 7157 (34.5%) genes that were annotated in only a single tissue. We found 2692 brain-enriched genes, while 2848 genes were liver-enriched, and 2007 genes were gonad-enriched. Furthermore, 6821 annotated genes were common to all tissues in both males and females (Figure 3). The gonad-enriched genes were enriched in the following GO terms: sexual reproduction and gamete generation. The brain-enriched genes were enriched in functions related to channel activity, synaptic transmission and cell-cell adhesion. The liver-enriched genes were enriched in functions related to metabolic processes, transferase and mannosidase activity (Table 2, Additional file 10: Table S10).Figure 3

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