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Gonadal transcriptome analysis in sterile double haploid Japanese flounder

ABSTRACT: We used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation,

ORGANISM(S): Paralichthys olivaceus

PROVIDER: GSE75895 | GEO | 2015/12/10

SECONDARY ACCESSION(S): PRJNA305624

REPOSITORIES: GEO

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Gonadal transcriptome analysis in sterile double haploid Japanese flounder

Project description:We used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation, Three sterile female japanese flounders were control samples and three fertile ones were references samples

2015-12-10 | E-GEOD-75895 | biostudies-arrayexpress

Gonadal Transcriptome Analysis in Sterile Double Haploid Japanese Flounder.

Project description:Sterility is a serious problem that can affect all bionts. In teleosts, double haploids (DHs) induced by mitogynogenesis are often sterile. This sterility severely restricts the further application of DHs for production of clones, genetic analysis, and breeding. However, sterile DH individuals are good source materials for investigation of the molecular mechanisms of gonad development, especially for studies into the role of genes that are indispensable for fish reproduction. Here, we used the Illumina sequencing platform to analyze the transcriptome of sterile female DH Japanese flounder in order to identify major genes that cause sterility and to provide a molecular basis for an intensive study of gonadal development in teleosts. Through sequencing, assembly, and annotation, we obtained 52,474 contigs and found that 60.7% of these shared homologies with existing sequences. A total of 1225 differentially expressed unigenes were found, including 492 upregulated and 733 downregulated genes. Gene Ontology and KEGG analyses showed that genes showing significant upregulation, such as CYP11A1, CYP11B2, CYP17, CYP21, HSD3?, bcl2l1, and PRLR, principally correlated with sterol metabolic process, steroid biosynthetic process, and the Jak-stat signaling pathway. The significantly downregulated genes were primarily associated with immune response, antigen processing and presentation, cytokine-cytokine receptor interaction, and protein digestion and absorption. Using a co-expression network analysis, we conducted a comprehensive comparison of gene expression in the gonads of fertile and sterile female DH Japanese flounder. Identification of genes showing significantly different expression will provide further insights into DH reproductive dysfunction and oocyte maturation processes in teleosts.

| S-EPMC4651314 | biostudies-literature

Identification and differential expression of microRNAs during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

2013-03-10 | GSE27986 | GEO

High-throughput sequencing of small RNA during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder.

2010-12-23 | GSE25995 | GEO

Identification and differential expression of microRNAs during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

Project description:The 987 probes (Japanese flounder conserved miRNAs and candidates, fish conserved miRNAs, and contro) were hybridized with two stages during Japanese flounder metamorphosis by miRNA microarray. We validated 92 miRNAs using miRNA microarray in the 17 dph and 29 dph of Japanese flounder development, and obtained 66 differertially expressed miRNAs by comparison miRNA expression patterns of the two stages. These results indicate that miRNAs might play key roles in regulating gene expression during Japanese flounder metamorphosis. Using miRNA microarray, the flounder conserved miRNAs and candidates were identified, and 92 conserved miRNAs were detected in the 17 dph and 29 dph during metamorphosis. Meanwhile, 66 conserved miRNAs were differertially expressed by comparison miRNA expression patterns of the two stages. We further identified flounder miRNAs during metamorphosis.

2013-03-10 | E-GEOD-27986 | biostudies-arrayexpress

High-throughput sequencing of small RNA during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

2010-12-23 | E-GEOD-25995 | biostudies-arrayexpress

The time-dependent global micro-transcriptome of Japanese flounder in response to Vibrio anguillarum infection

Project description:Japanese flounder (Paralichthys olivaceus) is an economic important aquaculture fish that was susceptible to Vibrio anguillarum. To fully deciphered the molecular mechanisms underlying flounder host defense against V. anguillarum infection, we perform the micro-transcriptome analysis of founder spleen with and without V. anguillarum infection at 3 time points.

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Gene expression profiles of vaccinated fish using a long-term efficiency mixed vaccine against Edwardsiella tarda performed by a new designed oligo DNA microarray in Japanese flounder Paralichthys olivaceus

Project description:Gene expression profiles by microarray have contributed for a elucidation of an immune-response and a determination of efficiency in vaccination. Recent day, edwardsielosis have caused a fatal damage in the aquaculture of Japanese flounder, Paralichthys olivaceus. However the formalin killed-cell vaccines made from Edwardsiella tarda isolated same fish species were not efficient. Recent our study revealed the mixed FKC vaccine made from the two different type of E. tarda protected Japanese flounder against Edwardsiella tarda infection for long-term. In this study, we analyzed the immune-response of a vaccinated fish kidney using the mixed FKC vaccine against Edwardsiella tarda with an Agilent custom-oligo DNA microarray on 9,573 probes of Japanese flounder. Our study revealed that the mixed FKC vaccine confered a strong immune-response and keeped a efficient for long-term on Japanese flounder.

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Paralichthys olivaceus breed:Japanese flounder

Project description:Paralichthys olivaceus breed:Japanese flounder Raw sequence reads

| PRJNA776544 | ENA

Gene expression profiles in kidney of Japanese flounder injected with formalin-killed bacterial cells

Project description:In order to identify the genes induced by different bacterial cells, which may contain different types of pathogen associated molecular patterns (PAMPs), high-throughput gene expression analyses using Agilent custom-oligo DNA microarray containingon 9,573 probes constructed for Japanese flounder Paralichthys olivaceus were conducted. A number of genes showed significant changes in mRNA levels. However, there are no significant difference in a manner of the changes among the different bacterial cell treatments. The genes significantly induced by the treatments included well-known immune-related genes such as granulocyte-colony stimulation factor, haptoglobin, hepcidin. The kidney were isolated from the formalin killed cells (FKCs) intraperitoneal injected Japanese flounder, Paralichthys olivaceus using the four formalin-killed cells, Edwardsiella tarda strain 54, Lactococcus garviae strain EH8706, Streptococcus iniae strain 02 and Vibrio anguillarum strain H775-3, respectively. Fishes were administered by an intraperitoneal injection using the 1.0 x 10^7 to 1.0 x 10^8 cells of FKCs. After 6 hours from a injection, fish kidney was isolated. We also isolated phosphate-bufferd seline injected fish kidney as a control. We analyzed a four samples in control. We also analyze a three samples in FKC injected fish (16 hybridization).

2014-12-11 | E-GEOD-29219 | biostudies-arrayexpress

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