Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, 29590, Málaga, Spain.
BMC Genomics. 2020 Jul 8;21(1):471. doi: 10.1186/s12864-020-06860-z.
Zebrafish 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.
We 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.
Orthologous 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.
斑马鱼是一种常用的模式生物，广泛应用于发育生物学研究。尽管其应用广泛，但斑马鱼和人类卵母细胞转录组的直接比较尚未得到很好的研究。观察这两种生物在基因序列水平上的相似性是否也在卵母细胞等关键细胞类型的表达水平上观察到，这一点很重要。
我们对斑马鱼卵母细胞进行了单细胞 RNA-seq 分析，并将其与两项已对人类卵母细胞进行单细胞 RNA-seq 的研究进行了比较。我们对卵母细胞中表达的基因和这三项研究中高表达的卵母细胞基因进行了比较分析。总体而言，我们发现人类研究之间具有高度一致性，并且这两种生物的同源基因在表达上也高度一致。根据 Ensembl 数据库，约 60%的人类蛋白编码基因与斑马鱼基因具有同源性。我们的结果表明，在这两个生物体中高表达的基因中，具有同源性的基因比例高于低表达的基因。对这三项研究中高表达基因的系统生物学分析显示，富集途径和 GO 术语有显著重叠。此外，这两种生物体中共同过表达的同源基因参与了对卵母细胞功能至关重要的生物学机制。
同源基因在这两种生物的卵母细胞中同时高度表达，并且这些基因属于相似的功能类别。我们的研究结果提供了证据表明，斑马鱼可以作为研究人类卵母细胞的有效模型生物，具有直接的人类应用意义。
