Data from: Transcriptomic signatures associated with underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae
Data files
Jul 21, 2023 version files 1.39 GB
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EggNog_All_Anno.tsv
226.78 MB
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README.md
1.18 KB
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RSEM.genes.results_Count_merge
13.46 MB
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RSEM.genes.results_TPM_merge
17.69 MB
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Trinity_v265_L20T20S420A20M100_onlyPepetide.fasta
216.10 MB
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Trinity_v265_L20T20S420A20M100.Trinity.fasta
911.83 MB
Oct 25, 2023 version files 1.39 GB
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EggNog_All_Anno.tsv
226.78 MB
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Expressoin_analysis_summary.R
32.36 KB
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README.md
1.71 KB
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RSEM.genes.results_Count_merge
13.46 MB
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RSEM.genes.results_TPM_merge
17.69 MB
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Trinity_v265_L20T20S420A20M100_onlyPepetide.fasta
216.10 MB
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Trinity_v265_L20T20S420A20M100.Trinity.fasta
911.83 MB
Abstract
Teleost fish exhibit remarkable sexual plasticity and divergent developmental systems, including hermaphroditism. One of the more fascinating models of sexual plasticity is socially controlled sex change, which is often observed in coral reef fish. The Okinawa rubble goby, Trimma okinawae, is a bi-directional sex-changing fish. It can rapidly change sex in either direction based on social circumstances. Although behavioral and neuroendocrine sex change occurs immediately and is believed to trigger gonadal changes, the underlying mechanisms remain poorly understood. In this study, we conducted a de novo transcriptome analysis of the T. okinawae brain and identified genes that are differentially expressed between the sexes and genes that were immediately controlled by social stimulation implicating sex change. Several genes showed concordant expression shifts regardless of the sex change direction and were associated with histone modification in nerve cells. These genes are known to function in the neuroendocrine control of reproduction in nerve cells. Overall, we identified genes associated with the initiation of sex change, which provides insight into the regulation of sex change and sexual plasticity.
We conducted a de novo transcriptome analysis of the T. okinawae brain to detect the genes immediately controlled by social stimulation causing a sex change. Subsequently, protein-coding sequences were detected with TransDecoder using default parameters and remove the redundancy using CD-hit. We used RSEM with bowtie2 as a mapping program to calculate the mRNA abundance of the individual samples. Also, those contigs coding proteins were annotated by EggNoG2.
Description of the data and file structure
Trinity_v265_L20T20S420A20M100.Trinity.fasta: The fasta file resulted from de-novo assembly using Trinity.
Trinity_v265_L20T20S420A20M100_onlyPepetide.fasta: The fasta file of putative protein-coding contigs filtered using TransDecoder and CD-hit.
EggNog_All_Anno.tsv: The annotation file of each protein coded in contigs using EggNOG2 mapper. The cells of “-“ in this file represent no data.
RSEM.genes.results_Count_merge: The count table of gene expression of each sample calculated by RSEM.
RSEM.genes.results_TPM_merge: The TPM table of gene expression of each sample calculated by RSEM.
Expressoin_analysis_summary.R: Summary of R code for expression analysis. The version of packages are below:
library(tidyverse) # v1.1.1
library(fs) # v1.6.2
library(devtools) # v2.4.5
library(ggbiplot) # v0.55
library(DESeq2) # v1.36.0
library(ggVennDiagram) # v1.2.2
library(pheatmap) # v1.0.12
library(ggrepel) # v0.9.3
library(pheatmap) # 1.0.12
library(RColorBrewer) # v1.1-3
library(viridis) # v0.6.3
library(ggbiplot) # v0.55
library(VennDiagram) # v1.7.3
library(geneLenDataBase) # v1.32.0
library(goseq) # v1.48.0
library(GO.db) # v3.15.0