Abstract
BackgroundSimilar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. However, systematic studies of the dimorphic patterns of gene expression in the brain of male and female zebrafish are lacking.ResultsIn this study, the mRNA and lncRNA expression profiles were obtained from the brain tissue samples of the three male and three female zebrafish by high-throughput transcriptome sequencing. We identified a total of 108 mRNAs and 50 lncRNAs with sex-based differential expression. We randomly selected four differentially expressed genes for RT-qPCR verification and the results certified that the expression pattern showed a similar trend between RNA-seq and RT-qPCR results. Protein-protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to obtain the biological significance of differentially expressed mRNA in the brain dimorphism of zebrafish. Finally, a Pearson correlation analysis was performed to construct the co-expression network of the mRNAs and lncRNAs.ConclusionsWe found that 12 new lncRNAs not only have significant gender specificity in the brain of zebrafish, and this finding may provide a clue to further study of the functional difference between male and female zebrafish brain.
Highlights
Similar to humans, the zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior
Sequencing data, raw data filtering, and mapping of RNA sequencing reads onto the zebrafish genome High-throughput sequencing generated 113.71 G bp of raw data (Additional file 1), and after filtering, the clean data of 98.52 G bp were extracted
Expressed genes We analyzed the transcriptome data of the six zebrafish brain tissue samples to obtain the sex-based gene expression of zebrafish in brain
Summary
The zebrafish brain plays a central role in regulating sexual reproduction, maturation and sexual behavior. The sex-related chromosomal regions of zebrafish are not fixed [2, 3] and their genome of different sexes can be very similar; we can observe its sexual dimorphism by differences in gene expression [4]. By. Long non-coding RNAs (long ncRNAs, lncRNAs), which may appear anywhere in the genome, are defined as transcripts longer than 200 nucleotides that are not. It was found that some regulatory genes and lncRNAs may play a key role in development and hematopoiesis through processing functional coupling network using deep RNA-seq sequencing [13]. A novel non-coding RNA, arising from the first exon of Kalirin, is a key player in axonal development in zebrafish and maintains dendritic length and density by regulating kalrna expression [14]. Many lncRNAs with biological functions have been found in zebrafish [15,16,17,18]; the function of the sex-based lncRNAs in the brain is still unknown
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