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

BMC Genomics
Keng Po LaiRudolf Shiu-Sun Wu

Abstract

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. 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 t...Continue Reading

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Citations

Jan 12, 2016·Aquatic Toxicology·Keng Po LaiRudolf Shiu-Sun Wu
Dec 31, 2015·Marine Environmental Research·Bo-Mi KimJae-Seong Lee
Mar 15, 2016·Biochimica Et Biophysica Acta·Marco Chi Chung LauWilliam Ka Fai Tse
Nov 8, 2015·Aquatic Toxicology·Natalie DeggerRudolf S S Wu
May 25, 2016·Scientific Reports·Jian Wang, Wen-Xiong Wang
Jul 17, 2016·Aquatic Toxicology·Keng Po LaiRudolf Shiu Sun Wu
Jul 5, 2016·Nature Communications·Simon Yuan WangRudolf Shiu-Sun Wu
Aug 27, 2016·Scientific Reports·Qin QiaoBenjamin Marie
Oct 22, 2016·Aquatic Toxicology·Anna Chung-Kwan TseRudolf Shiu-Sun Wu
Jan 31, 2017·Environmental Pollution·Keng Po LaiChris Kong Chu Wong
Jun 28, 2017·Environmental Science & Technology·Keng Po LaiChris Kong-Chu Wong
Feb 17, 2018·Molecular Ecology Resources·Hui-Su KimJae-Seong Lee
Jul 4, 2020·Environmental Microbiology·Keng Po LaiWilliam Ka Fai Tse
Jan 29, 2021·Ecotoxicology and Environmental Safety·Deliang YuXiao Peng
Mar 8, 2019·Environmental Science & Technology·Keng Po LaiRudolf Shiu Sun Wu

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Datasets Mentioned

BETA
SRP004363
SRP032993
SRP041838
GBFY00000000
GBFS00000000
GBGE00000000
246584

Methods Mentioned

BETA
RNA-Seq
PCR
environmental stresses

Software Mentioned

MEM
hit
Trinity
BLASTp
BinGO
Ensemble Assembly
BLASTn
TMHMM
BLASTx
Ensembl

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