Limits...
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.

Show MeSH

Related in: MedlinePlus

Transcriptome divergence between marine and freshwater medaka. A) Nucleotide identity between Oryzias melastigma and Oryzias latipes orthologs deposited in the NCBI nucleotide database. Only those with an alignment length >75% are shown. B) Nucleotide identity between all O. melastigma and O. latipes orthologs. C) Low mapping rate of O. melastigma RNA-Seq data generated in this study onto the O. latipes UniGENE dataset. The mapping rate is highest for liver and lowest for brain. D) The nucleotide identity between transcripts (Ensemble Assembly) assembled in this study and the O. latipes UniGENE dataset. Only those with alignment length >75% are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Transcriptome divergence between marine and freshwater medaka. A) Nucleotide identity between Oryzias melastigma and Oryzias latipes orthologs deposited in the NCBI nucleotide database. Only those with an alignment length >75% are shown. B) Nucleotide identity between all O. melastigma and O. latipes orthologs. C) Low mapping rate of O. melastigma RNA-Seq data generated in this study onto the O. latipes UniGENE dataset. The mapping rate is highest for liver and lowest for brain. D) The nucleotide identity between transcripts (Ensemble Assembly) assembled in this study and the O. latipes UniGENE dataset. Only those with alignment length >75% are shown.

Mentions: 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. Based on the mRNA transcripts deposited in the NCBI nucleotide database, orthologs in O. melastigma and O. latipes were identified using Reciprocal BLAST. The reciprocal best hit (RBH) was found for 58.6% (211/360) of the O. melastigma transcripts. Among the RBHs, the average identity was 91.5% (median: 91.8%), suggesting an extensive diversity between the two species. (Figure 2A-B). In line with our observation, phylogeographic studies of medaka using allozymes and mitochondrial DNA sequences have revealed a genetic diversity in the Oryzias family [34-36]. The studies showed that wild populations of medaka were divided into four major regionally differentiated groups and the Nei’s genetic distances among these groups are very large (0.35-0.88).Figure 2


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)

Transcriptome divergence between marine and freshwater medaka. A) Nucleotide identity between Oryzias melastigma and Oryzias latipes orthologs deposited in the NCBI nucleotide database. Only those with an alignment length >75% are shown. B) Nucleotide identity between all O. melastigma and O. latipes orthologs. C) Low mapping rate of O. melastigma RNA-Seq data generated in this study onto the O. latipes UniGENE dataset. The mapping rate is highest for liver and lowest for brain. D) The nucleotide identity between transcripts (Ensemble Assembly) assembled in this study and the O. latipes UniGENE dataset. Only those with alignment length >75% are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Transcriptome divergence between marine and freshwater medaka. A) Nucleotide identity between Oryzias melastigma and Oryzias latipes orthologs deposited in the NCBI nucleotide database. Only those with an alignment length >75% are shown. B) Nucleotide identity between all O. melastigma and O. latipes orthologs. C) Low mapping rate of O. melastigma RNA-Seq data generated in this study onto the O. latipes UniGENE dataset. The mapping rate is highest for liver and lowest for brain. D) The nucleotide identity between transcripts (Ensemble Assembly) assembled in this study and the O. latipes UniGENE dataset. Only those with alignment length >75% are shown.
Mentions: 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. Based on the mRNA transcripts deposited in the NCBI nucleotide database, orthologs in O. melastigma and O. latipes were identified using Reciprocal BLAST. The reciprocal best hit (RBH) was found for 58.6% (211/360) of the O. melastigma transcripts. Among the RBHs, the average identity was 91.5% (median: 91.8%), suggesting an extensive diversity between the two species. (Figure 2A-B). In line with our observation, phylogeographic studies of medaka using allozymes and mitochondrial DNA sequences have revealed a genetic diversity in the Oryzias family [34-36]. The studies showed that wild populations of medaka were divided into four major regionally differentiated groups and the Nei’s genetic distances among these groups are very large (0.35-0.88).Figure 2

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