Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes
Abstract Background 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 th...
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| Format: | Article |
| Language: | English |
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BMC
2020-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-06860-z |
| _version_ | 1818776052129857536 |
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| author | Handan Can Sree K. Chanumolu Elena Gonzalez-Muñoz Sukumal Prukudom Hasan H. Otu Jose B. Cibelli |
| author_facet | Handan Can Sree K. Chanumolu Elena Gonzalez-Muñoz Sukumal Prukudom Hasan H. Otu Jose B. Cibelli |
| author_sort | Handan Can |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| first_indexed | 2024-12-18T11:06:48Z |
| format | Article |
| id | doaj.art-eb43edfa0ca54c2fa501b0ad2d4803fa |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T11:06:48Z |
| publishDate | 2020-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-eb43edfa0ca54c2fa501b0ad2d4803fa2022-12-21T21:10:06ZengBMCBMC Genomics1471-21642020-07-0121111510.1186/s12864-020-06860-zComparative analysis of single-cell transcriptomics in human and Zebrafish oocytesHandan Can0Sree K. Chanumolu1Elena Gonzalez-Muñoz2Sukumal Prukudom3Hasan H. Otu4Jose B. Cibelli5Department of Electrical and Computer Engineering, University of Nebraska-LincolnDepartment of Electrical and Computer Engineering, University of Nebraska-LincolnLARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONANDDepartment of Anatomy, Faculty of Veterinary Medicine, Kasetsart UniversityDepartment of Electrical and Computer Engineering, University of Nebraska-LincolnDepartments of Animal Science and Large Animal Clinical Sciences, Michigan State UniversityAbstract Background 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. Results 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. Conclusions 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.http://link.springer.com/article/10.1186/s12864-020-06860-zZebrafishOocyteOrthologyRNA-seqTranscriptome |
| spellingShingle | Handan Can Sree K. Chanumolu Elena Gonzalez-Muñoz Sukumal Prukudom Hasan H. Otu Jose B. Cibelli Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes BMC Genomics Zebrafish Oocyte Orthology RNA-seq Transcriptome |
| title | Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes |
| title_full | Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes |
| title_fullStr | Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes |
| title_full_unstemmed | Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes |
| title_short | Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes |
| title_sort | comparative analysis of single cell transcriptomics in human and zebrafish oocytes |
| topic | Zebrafish Oocyte Orthology RNA-seq Transcriptome |
| url | http://link.springer.com/article/10.1186/s12864-020-06860-z |
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