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| Status |
Public on May 01, 2024 |
| Title |
Molecular characterization and differential expression profiles of transcription factor Sox gene family between ovaries and testes from golden pompano （Trachinotus ovatus） |
| Organism |
Trachinotus ovatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The SRY-related HMG-box (Sox) is a transcription factor related to the testis-determining gene SRY (Sex determination Region of Y chromosome), which plays an important role in the sexual development of Osteichthyes. In order to understand the characteristics of Sox gene family members in Trachinotus ovatus（ToSox）, this study used bioinformatics methods to systematically analyze the physicochemical properties, phylogenetic tree, chromosomal localization, and prediction of interacting proteins of the ToSsxs. The expressions of the ToSoxs were analyzed using transcriptomics data from ovary and testis of T. ovatus. The results showed that 18 members of Sox gene family were identified, and the members of the family were hydrophilic proteins with large differences in amino acid number, molecular weight and isoelectric point. The evolutionary tree analysis showed that the Sox family genes were divided into seven branches (B1, B2, C, D, E, F, H) The chromosomal localization analysis showed that these genes of the family were scattered on 15 chromosomes. The structure of Sox genes was simple and relatively conserved. Intraspecific covariance analysis revealed that one pair of ToSox gene covariance, and interspecific covariance analysis revealed 14 pairs of collinearities between T. ovatus and zebrafish and 20 pairs of collinearities between T. ovatus and tilapia. The members of ToSox proteins had close interactions with one another, and with other proteins as well. The results of transcriptome analysis showed that the genes ToSox30, ToSox1a, ToSox17, ToSox11, ToSox9b, and ToSox9b are likely to regulate the testicular development of oviparous jacks, which is related to male sex determination. This study preliminarily investigated the characterization of Sox genes in the T. ovatus genome and provided theoretical references for the study of the effects of Sox transcription factors on sex determination in T. ovatus.
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| Overall design |
The testes of three male golden pompano and the ovaries of three female golden pompano were taken from the Shenzhen Experimental Base of the South China Sea Fisheries Research Institute (SCFRRI) for transcriptome data determination.
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| Contributor(s) |
Chen R, Pan J, Guo H, Zhang D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 26, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Honghua Chen |
| E-mail(s) |
19876388857m@sina.cn
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| Phone |
19876388857
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| Organization name |
Chinese Academy of Fishery Sciences
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| Street address |
Haizhu District - 6-7/F, Xinhai Building, No. 231 Xingang West Road
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| City |
Guangzhou |
| ZIP/Postal code |
510300 |
| Country |
China |
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| Platforms (1) |
| GPL34418 |
Illumina NovaSeq 6000 (Trachinotus ovatus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA1105006 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE265938_anno_genes.FPKM.txt.gz |
928.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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