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Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole ( Cynoglossus semilaevis ) Revealed by Brain Transcriptome Analysis

View Article: PubMed Central - PubMed

ABSTRACT

In this study, we performed a comprehensive analysis of the transcriptome of one- and two-year-old male and female brains of Cynoglossus semilaevis by high-throughput Illumina sequencing. A total of 77,066 transcripts, corresponding to 21,475 unigenes, were obtained with a N50 value of 4349 bp. Of these unigenes, 33 genes were found to have significant differential expression and potentially associated with growth, from which 18 genes were down-regulated and 12 genes were up-regulated in two-year-old males, most of these genes had no significant differences in expression among one-year-old males and females and two-year-old females. A similar analysis was conducted to look for genes associated with reproduction; 25 genes were identified, among them, five genes were found to be down regulated and 20 genes up regulated in two-year-old males, again, most of the genes had no significant expression differences among the other three. The performance of up regulated genes in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was significantly different between two-year-old males and females. Males had a high gene expression in genetic information processing, while female’s highly expressed genes were mainly enriched on organismal systems. Our work identified a set of sex-biased genes potentially associated with growth and reproduction that might be the candidate factors affecting sexual dimorphism of tongue sole, laying the foundation to understand the complex process of sex determination of this economic valuable species.

No MeSH data available.


Brain transcriptome validation by qPCR using eleven selected genes: (A) Gene relative expression in qPCR where Error bars represent standard deviation of technical replicates and the expression differences between M2 and F2 were tested by two-tailed Student’s t-test, with 95% confidence level (p < 0.05) being labeled with an asterisk; and (B) gene expression in RNA-Seq.
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ijms-17-01402-f003: Brain transcriptome validation by qPCR using eleven selected genes: (A) Gene relative expression in qPCR where Error bars represent standard deviation of technical replicates and the expression differences between M2 and F2 were tested by two-tailed Student’s t-test, with 95% confidence level (p < 0.05) being labeled with an asterisk; and (B) gene expression in RNA-Seq.

Mentions: In order to validate the expression pattern of DEGs identified by RNA-Sequencing, we randomly selected eleven genes from DEGs potentially associated with growth or reproduction (Table 2 and Table 3) for qPCR validation, including vdac2, ccnblip1, ropn1l, exosc9, cct7, mdk, ywhaq, gap43, cxcl12b, foxb1 and spin1. M2 was used as the reference in 2−∆∆Ct method to calculate the relative gene expression level. Comparing the relative expression level of eleven selected genes, most results of qPCR were consistent with the results of RNA-Seq (Figure 3). The Pearson’s correlation of log10(fold-change) between qPCR and RNA-Seq was 0.80, indicating the accuracy and reliability of RNA-Seq based transcriptome analysis.


Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole ( Cynoglossus semilaevis ) Revealed by Brain Transcriptome Analysis
Brain transcriptome validation by qPCR using eleven selected genes: (A) Gene relative expression in qPCR where Error bars represent standard deviation of technical replicates and the expression differences between M2 and F2 were tested by two-tailed Student’s t-test, with 95% confidence level (p < 0.05) being labeled with an asterisk; and (B) gene expression in RNA-Seq.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5037682&req=5

ijms-17-01402-f003: Brain transcriptome validation by qPCR using eleven selected genes: (A) Gene relative expression in qPCR where Error bars represent standard deviation of technical replicates and the expression differences between M2 and F2 were tested by two-tailed Student’s t-test, with 95% confidence level (p < 0.05) being labeled with an asterisk; and (B) gene expression in RNA-Seq.
Mentions: In order to validate the expression pattern of DEGs identified by RNA-Sequencing, we randomly selected eleven genes from DEGs potentially associated with growth or reproduction (Table 2 and Table 3) for qPCR validation, including vdac2, ccnblip1, ropn1l, exosc9, cct7, mdk, ywhaq, gap43, cxcl12b, foxb1 and spin1. M2 was used as the reference in 2−∆∆Ct method to calculate the relative gene expression level. Comparing the relative expression level of eleven selected genes, most results of qPCR were consistent with the results of RNA-Seq (Figure 3). The Pearson’s correlation of log10(fold-change) between qPCR and RNA-Seq was 0.80, indicating the accuracy and reliability of RNA-Seq based transcriptome analysis.

View Article: PubMed Central - PubMed

ABSTRACT

In this study, we performed a comprehensive analysis of the transcriptome of one- and two-year-old male and female brains of Cynoglossus semilaevis by high-throughput Illumina sequencing. A total of 77,066 transcripts, corresponding to 21,475 unigenes, were obtained with a N50 value of 4349 bp. Of these unigenes, 33 genes were found to have significant differential expression and potentially associated with growth, from which 18 genes were down-regulated and 12 genes were up-regulated in two-year-old males, most of these genes had no significant differences in expression among one-year-old males and females and two-year-old females. A similar analysis was conducted to look for genes associated with reproduction; 25 genes were identified, among them, five genes were found to be down regulated and 20 genes up regulated in two-year-old males, again, most of the genes had no significant expression differences among the other three. The performance of up regulated genes in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was significantly different between two-year-old males and females. Males had a high gene expression in genetic information processing, while female&rsquo;s highly expressed genes were mainly enriched on organismal systems. Our work identified a set of sex-biased genes potentially associated with growth and reproduction that might be the candidate factors affecting sexual dimorphism of tongue sole, laying the foundation to understand the complex process of sex determination of this economic valuable species.

No MeSH data available.