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

Keng P.o. Lai, Jing Woei Li, Simon Y.uan Wang, Jill M.an Ying Chiu, Anna Tse, Karen Lau, Si Lok, Doris W.ai Ting Au, William K.a.Fai Tse, Chris K.ong Chu Wong, Ting Fung Chan, Richard Y.uen Chong Kong, Rudolf S.hiu Sun Wu

Research output: Contribution to journalArticle

29 Citations (Scopus)

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.

Original languageEnglish
Number of pages1
JournalBMC Genomics
Volume16
DOIs
Publication statusPublished - Jan 1 2015

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Oryzias
Fresh Water
Transcriptome
Testis
Ovary
Genome
Genes
Molecular Sequence Annotation
High-Throughput Nucleotide Sequencing
Gene Ontology
Liver
Brain

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

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Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. / Lai, Keng P.o.; Li, Jing Woei; Wang, Simon Y.uan; Chiu, Jill M.an Ying; Tse, Anna; Lau, Karen; Lok, Si; Au, Doris W.ai Ting; Tse, William K.a.Fai; Wong, Chris K.ong Chu; Chan, Ting Fung; Kong, Richard Y.uen Chong; Wu, Rudolf S.hiu Sun.

In: BMC Genomics, Vol. 16, 01.01.2015.

Research output: Contribution to journalArticle

Lai, Keng P.o. ; Li, Jing Woei ; Wang, Simon Y.uan ; Chiu, Jill M.an Ying ; Tse, Anna ; Lau, Karen ; Lok, Si ; Au, Doris W.ai Ting ; Tse, William K.a.Fai ; Wong, Chris K.ong Chu ; Chan, Ting Fung ; Kong, Richard Y.uen Chong ; Wu, Rudolf S.hiu Sun. / Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes. In: BMC Genomics. 2015 ; Vol. 16.
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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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T1 - Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes

AU - Lai, Keng P.o.

AU - Li, Jing Woei

AU - Wang, Simon Y.uan

AU - Chiu, Jill M.an Ying

AU - Tse, Anna

AU - Lau, Karen

AU - Lok, Si

AU - Au, Doris W.ai Ting

AU - Tse, William K.a.Fai

AU - Wong, Chris K.ong Chu

AU - Chan, Ting Fung

AU - Kong, Richard Y.uen Chong

AU - Wu, Rudolf S.hiu Sun

PY - 2015/1/1

Y1 - 2015/1/1

N2 - 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.

AB - 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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U2 - 10.1186/s12864-015-1325-7

DO - 10.1186/s12864-015-1325-7

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JO - BMC Genomics

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