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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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Validation ofO.melastigma-enrichedgenes by RT-PCR. The marine medaka specific genes were validated in both male and female marine medaka against freshwater medaka.
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Fig5: Validation ofO.melastigma-enrichedgenes by RT-PCR. The marine medaka specific genes were validated in both male and female marine medaka against freshwater medaka.

Mentions: Furthermore, by using read-count approach and qPCR validation, we estimated that a lower boundary of 255 genes being only expressed in O. melastigma compared to those in the O. latipes database (Additional file 12: Table S12). The highly expressed genes in O. melastigma and some selected genes that might be functionally related to seawater adaptation were further validated by RT-PCR. Indeed, our results showed that a number of genes were highly expressed in O. melastigma but undetected in O. latipes (FigureĀ 5). One of the O. melastigma-enriched genes, solute carrier and organic anion transporter (SO3A1), is commonly found in human brain tissue and epidermal keratinocytes. SO3A1 may play a role in the exchange of anions between cells, thus facilitating seawater adaptation [55]. In addition, it mediates the transport of thyroxine and vasopressin [56] that is important in osmoregulation [57,58]. Similarly, another solute carrier, solute carrier family 12 member 5 (S12A5), is commonly found in brain. It is a potassium-chloride co-transporter, which is highly expressed in neurons [59]. In addition, the sodium-calcium-potassium exchanger 2 (NCKX2) is a polytopic membrane protein that drives Ca2+ extrusion across the plasma membrane [60]. All these three transporters mentioned above are highly expressed in the brain region. However, they all cannot be aligned in the recent existing freshwater medaka. Additionally, cardiac channels such as potassium voltage-gated channel subfamily D member 2 (KCND2) and plakophilin-2 (PKP2) also only be found in the marine medaka. KCND2 is critical in repolarizing the cardiac action potential [61], while PKP2 is essential protein for building up of desmosome. PKP2 has been reported to be functionally related to sodium channel, and decreased in PKP2 expression leaded to downregulation of sodium current in cardiomyocytes of human [62,63]. The data presented here, hence provides opportunities for researchers to understand the ion transporters mechanism between two species by using our database as nucleotide references for different molecular probes.Figure 5


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)

Validation ofO.melastigma-enrichedgenes by RT-PCR. The marine medaka specific genes were validated in both male and female marine medaka against freshwater medaka.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Validation ofO.melastigma-enrichedgenes by RT-PCR. The marine medaka specific genes were validated in both male and female marine medaka against freshwater medaka.
Mentions: Furthermore, by using read-count approach and qPCR validation, we estimated that a lower boundary of 255 genes being only expressed in O. melastigma compared to those in the O. latipes database (Additional file 12: Table S12). The highly expressed genes in O. melastigma and some selected genes that might be functionally related to seawater adaptation were further validated by RT-PCR. Indeed, our results showed that a number of genes were highly expressed in O. melastigma but undetected in O. latipes (FigureĀ 5). One of the O. melastigma-enriched genes, solute carrier and organic anion transporter (SO3A1), is commonly found in human brain tissue and epidermal keratinocytes. SO3A1 may play a role in the exchange of anions between cells, thus facilitating seawater adaptation [55]. In addition, it mediates the transport of thyroxine and vasopressin [56] that is important in osmoregulation [57,58]. Similarly, another solute carrier, solute carrier family 12 member 5 (S12A5), is commonly found in brain. It is a potassium-chloride co-transporter, which is highly expressed in neurons [59]. In addition, the sodium-calcium-potassium exchanger 2 (NCKX2) is a polytopic membrane protein that drives Ca2+ extrusion across the plasma membrane [60]. All these three transporters mentioned above are highly expressed in the brain region. However, they all cannot be aligned in the recent existing freshwater medaka. Additionally, cardiac channels such as potassium voltage-gated channel subfamily D member 2 (KCND2) and plakophilin-2 (PKP2) also only be found in the marine medaka. KCND2 is critical in repolarizing the cardiac action potential [61], while PKP2 is essential protein for building up of desmosome. PKP2 has been reported to be functionally related to sodium channel, and decreased in PKP2 expression leaded to downregulation of sodium current in cardiomyocytes of human [62,63]. The data presented here, hence provides opportunities for researchers to understand the ion transporters mechanism between two species by using our database as nucleotide references for different molecular probes.Figure 5

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