Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development
Abstract Background Fish scales are typical products of biomineralization and play an important role in the adaptation of fish to their environment. The Gymnocypris przewalskii scales are highly specialized, with scales embedded in only specific parts of the dermis, such as the areas around the anal...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-10047-1 |
| _version_ | 1827328545769127936 |
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| author | Baoke Xu Yanrong Cui Linlin A. Haichen Zhang Qinghua Ma Fulei Wei Jian Liang |
| author_facet | Baoke Xu Yanrong Cui Linlin A. Haichen Zhang Qinghua Ma Fulei Wei Jian Liang |
| author_sort | Baoke Xu |
| collection | DOAJ |
| description | Abstract Background Fish scales are typical products of biomineralization and play an important role in the adaptation of fish to their environment. The Gymnocypris przewalskii scales are highly specialized, with scales embedded in only specific parts of the dermis, such as the areas around the anal fin and branchiostegite, making G. przewalskii an ideal material for biomineralization research. In this study, we aimed to unveil genes and pathways controlling scale formation through an integrated analysis of both transcriptome and proteome, of which G. przewalskii tissues of the dorsal skin (no scales) and the rump side skin (with scales) were sequenced. The sequencing results were further combined with cellular experiments to clarify the relationship between genes and signaling pathways. Results The results indicated the following: (1) a total of 4,904 differentially expressed genes were screened out, including 3,294 upregulated genes and 1,610 downregulated genes (with a filtering threshold of |log2Fold-Change|> 1 and p-adjust < 0.05). The identified differentially expressed genes contained family members such as FGF, EDAR, Wnt10, and bmp. (2) A total of 535 differentially expressed proteins (DEPs) were filtered out from the proteome, with 204 DEPs downregulated and 331 DEPs upregulated (with a filtering threshold of |Fold-Change|> 1.5 and p < 0.05). (3) Integrated analyses of transcriptome and proteome revealed that emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were important genes contributing to scale development and that PI3K-AKT was the most important signaling pathway involved. (4) With the use of the constructed G. przewalskii fibroblast cell line, emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were confirmed to be positively regulated by the PI3K-AKT signaling pathway. Conclusion This study provides experimental evidence for PI3K-AKT controlled scale development in G. przewalskii and would benefit further study on stress adaptation, scale biomineralization, and the development of skin appendages. |
| first_indexed | 2024-03-07T15:19:14Z |
| format | Article |
| id | doaj.art-ae0f3e9472aa4a17a657396a22bdf07a |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:19:14Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ae0f3e9472aa4a17a657396a22bdf07a2024-03-05T17:46:42ZengBMCBMC Genomics1471-21642024-02-0125111910.1186/s12864-024-10047-1Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale developmentBaoke Xu0Yanrong Cui1Linlin A.2Haichen Zhang3Qinghua Ma4Fulei Wei5Jian Liang6State Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityState Key Laboratory of Plateau Ecology and Agriculture, Qinghai UniversityAbstract Background Fish scales are typical products of biomineralization and play an important role in the adaptation of fish to their environment. The Gymnocypris przewalskii scales are highly specialized, with scales embedded in only specific parts of the dermis, such as the areas around the anal fin and branchiostegite, making G. przewalskii an ideal material for biomineralization research. In this study, we aimed to unveil genes and pathways controlling scale formation through an integrated analysis of both transcriptome and proteome, of which G. przewalskii tissues of the dorsal skin (no scales) and the rump side skin (with scales) were sequenced. The sequencing results were further combined with cellular experiments to clarify the relationship between genes and signaling pathways. Results The results indicated the following: (1) a total of 4,904 differentially expressed genes were screened out, including 3,294 upregulated genes and 1,610 downregulated genes (with a filtering threshold of |log2Fold-Change|> 1 and p-adjust < 0.05). The identified differentially expressed genes contained family members such as FGF, EDAR, Wnt10, and bmp. (2) A total of 535 differentially expressed proteins (DEPs) were filtered out from the proteome, with 204 DEPs downregulated and 331 DEPs upregulated (with a filtering threshold of |Fold-Change|> 1.5 and p < 0.05). (3) Integrated analyses of transcriptome and proteome revealed that emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were important genes contributing to scale development and that PI3K-AKT was the most important signaling pathway involved. (4) With the use of the constructed G. przewalskii fibroblast cell line, emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were confirmed to be positively regulated by the PI3K-AKT signaling pathway. Conclusion This study provides experimental evidence for PI3K-AKT controlled scale development in G. przewalskii and would benefit further study on stress adaptation, scale biomineralization, and the development of skin appendages.https://doi.org/10.1186/s12864-024-10047-1Gymnocypris przewalskiiScale developmentTranscriptomeProteome |
| spellingShingle | Baoke Xu Yanrong Cui Linlin A. Haichen Zhang Qinghua Ma Fulei Wei Jian Liang Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development BMC Genomics Gymnocypris przewalskii Scale development Transcriptome Proteome |
| title | Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development |
| title_full | Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development |
| title_fullStr | Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development |
| title_full_unstemmed | Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development |
| title_short | Transcriptomic and proteomic strategies to reveal the mechanism of Gymnocypris przewalskii scale development |
| title_sort | transcriptomic and proteomic strategies to reveal the mechanism of gymnocypris przewalskii scale development |
| topic | Gymnocypris przewalskii Scale development Transcriptome Proteome |
| url | https://doi.org/10.1186/s12864-024-10047-1 |
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