Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective
Genetic composition plays a crucial role in the growth rate of species, and transcriptomics provides a potent tool for studying genetic aspects of growth. We explored the growth rates and transcriptomes of the Cyprinids <i>G. przewalskii</i> (GP) and <i>G. eckloni</i> (GE). A...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-02-01
|
| Series: | Fishes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2410-3888/9/3/89 |
| _version_ | 1797241042198593536 |
|---|---|
| author | Yun Zhao Junming Zhou |
| author_facet | Yun Zhao Junming Zhou |
| author_sort | Yun Zhao |
| collection | DOAJ |
| description | Genetic composition plays a crucial role in the growth rate of species, and transcriptomics provides a potent tool for studying genetic aspects of growth. We explored the growth rates and transcriptomes of the Cyprinids <i>G. przewalskii</i> (GP) and <i>G. eckloni</i> (GE). A total of 500 individuals of <i>G. przewalskii</i> and <i>G. eckloni</i>, matched in size, were separately cultured for 9 months in six cement tanks (each group with three replicates). Growth indices were measured, revealing that the growth rate of GE was greater than that of GP (<i>p</i> < 0.05), while there was no significant difference in survival rates (<i>p</i> > 0.05). Simultaneously, we conducted RNA-Seq on the muscles of both GP and GE. The results indicated a significant difference of gene expression between GP and GE, identifying 5574 differentially expressed genes (DEGs). Quantitative real-time reverse transcription–polymerase chain reaction of 10 DEGs demonstrated consistency in expression profiles with the results from the RNA-Seq analysis. The DEGs were significantly enriched in glycolysis/gluconeogenesis (ko00010), arachidonic acid formation (ko00061), arginine biosynthesis (ko00220), and the MAPK (ko04013), PI3K-Akt (ko04151), mTOR (ko04150), and TGF-β (ko04350) signal pathways, as revealed by Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. This study also identified some growth-related DEGs, such as <i>IGF2</i>, <i>Noggin</i>, <i>Decorin</i> and others. Notably, the low expression of <i>IGF2</i> may be a factor contributing to the slower growth of GP than GE. |
| first_indexed | 2024-04-24T18:17:02Z |
| format | Article |
| id | doaj.art-8070dac040ff4a2c9173dc3bff0f2b8a |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-04-24T18:17:02Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Fishes |
| spelling | doaj.art-8070dac040ff4a2c9173dc3bff0f2b8a2024-03-27T13:38:17ZengMDPI AGFishes2410-38882024-02-01938910.3390/fishes9030089Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome PerspectiveYun Zhao0Junming Zhou1Key Laboratory of Plateau Wetland Ecology and Environmental Protection, Xichang University, Xichang 615013, ChinaKey Laboratory of Plateau Wetland Ecology and Environmental Protection, Xichang University, Xichang 615013, ChinaGenetic composition plays a crucial role in the growth rate of species, and transcriptomics provides a potent tool for studying genetic aspects of growth. We explored the growth rates and transcriptomes of the Cyprinids <i>G. przewalskii</i> (GP) and <i>G. eckloni</i> (GE). A total of 500 individuals of <i>G. przewalskii</i> and <i>G. eckloni</i>, matched in size, were separately cultured for 9 months in six cement tanks (each group with three replicates). Growth indices were measured, revealing that the growth rate of GE was greater than that of GP (<i>p</i> < 0.05), while there was no significant difference in survival rates (<i>p</i> > 0.05). Simultaneously, we conducted RNA-Seq on the muscles of both GP and GE. The results indicated a significant difference of gene expression between GP and GE, identifying 5574 differentially expressed genes (DEGs). Quantitative real-time reverse transcription–polymerase chain reaction of 10 DEGs demonstrated consistency in expression profiles with the results from the RNA-Seq analysis. The DEGs were significantly enriched in glycolysis/gluconeogenesis (ko00010), arachidonic acid formation (ko00061), arginine biosynthesis (ko00220), and the MAPK (ko04013), PI3K-Akt (ko04151), mTOR (ko04150), and TGF-β (ko04350) signal pathways, as revealed by Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. This study also identified some growth-related DEGs, such as <i>IGF2</i>, <i>Noggin</i>, <i>Decorin</i> and others. Notably, the low expression of <i>IGF2</i> may be a factor contributing to the slower growth of GP than GE.https://www.mdpi.com/2410-3888/9/3/89growth ratetranscriptome<i>Gymnocypris eckloni</i><i>Gymnocypris przewalskii</i> |
| spellingShingle | Yun Zhao Junming Zhou Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective Fishes growth rate transcriptome <i>Gymnocypris eckloni</i> <i>Gymnocypris przewalskii</i> |
| title | Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective |
| title_full | Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective |
| title_fullStr | Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective |
| title_full_unstemmed | Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective |
| title_short | Molecular Mechanisms of Growth Differences in <i>Gymnocypris przewalskii</i> and <i>Gymnocypris eckloni</i> through a Comparative Transcriptome Perspective |
| title_sort | molecular mechanisms of growth differences in i gymnocypris przewalskii i and i gymnocypris eckloni i through a comparative transcriptome perspective |
| topic | growth rate transcriptome <i>Gymnocypris eckloni</i> <i>Gymnocypris przewalskii</i> |
| url | https://www.mdpi.com/2410-3888/9/3/89 |
| work_keys_str_mv | AT yunzhao molecularmechanismsofgrowthdifferencesinigymnocyprisprzewalskiiiandigymnocypriseckloniithroughacomparativetranscriptomeperspective AT junmingzhou molecularmechanismsofgrowthdifferencesinigymnocyprisprzewalskiiiandigymnocypriseckloniithroughacomparativetranscriptomeperspective |