Abstract
BackgroundZebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.ResultsWe performed single-cell RNA-seq of the zebrafish oocyte and compared it with two studies that have performed single-cell RNA-seq of the human oocyte. We carried out a comparative analysis of genes expressed in the oocyte and genes highly expressed in the oocyte across the three studies. Overall, we found high consistency between the human studies and high concordance in expression for the orthologous genes in the two organisms. According to the Ensembl database, about 60% of the human protein coding genes are orthologous to the zebrafish genes. Our results showed that a higher percentage of the genes that are highly expressed in both organisms show orthology compared to the lower expressed genes. Systems biology analysis of the genes highly expressed in the three studies showed significant overlap of the enriched pathways and GO terms. Moreover, orthologous genes that are commonly overexpressed in both organisms were involved in biological mechanisms that are functionally essential to the oocyte.ConclusionsOrthologous genes are concurrently highly expressed in the oocytes of the two organisms and these genes belong to similar functional categories. Our results provide evidence that zebrafish could serve as a valid model organism to study the oocyte with direct implications in human.
Highlights
Zebrafish is a popular model organism, which is widely used in developmental biology research
Gene expression by type Our data analysis involve three single-cell RNA-seq datasets for the oocyte, each with three samples: zebrafish data generated by our group (ZF), human dataset 1 (H1) [12] and human dataset 2 (H2) [13]
Among the genes expressed in the zebrafish egg, and not expressed in the human oocytes or with no orthologue in human, we found members of the family of the elongation of very long-chain fatty acid (Elovl) genes ELOVL1A, 8B, 7B, 6 L, 1B, and 4B; and those highly expressed were Oogenesis-related gene (ORG), Claudin d (CLDND), Claudin g (CLDNG), and High mobility group box 3b (HMGB3B), in agreement with previous reports [20,21,22,23]
Summary
Zebrafish is a popular model organism, which is widely used in developmental biology research. The direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is observed at the expression level in key cell types such as the oocyte. The implementation of zebrafish (Danio rerio) as an animal model to study human disease is growing at an unprecedented pace [1]. The fact that its embryo is transparent, placed zebrafish as one of the main vertebrate models to study developmental processes [8]. We sought to compare the transcriptome profile of the single matured human and unfertilized zebrafish oocytes at the time of ovulation.
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