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Series GSE254010 Query DataSets for GSE254010
Status Public on May 17, 2024
Title Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction
Organisms Carassius auratus; Cyprinus carpio; Carassius gibelio
Experiment type Expression profiling by high throughput sequencing
Summary Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries), and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allow for their stable coexistence, integrating the evolutionary and ecological advantages and disadvantages of the two reproductive forms. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.
 
Overall design Here, the molecular mechanisms associated with reproduction in C. gibelio were analysed to study the coexistence of asexual and sexual forms. In particular, the expression of reproduction-related genes was expected to differ between asexual and sexual females, since meiosis-related genes are not important for asexually reproducing individuals. To test this hypothesis, transcriptome profile analyses of gonadal tissues (ovaries) from asexual females and sexual females of C. gibelio were performed. In addition, the transcriptomes of the closely-associated species C. carpio and C. auratus were also analysed, with a particular emphasis on the genes contributing to sexual reproduction.
 
Contributor(s) Jacques F, Tichopád T, Demko M, Bystrý V, Civáňová Křížová K, Seifertová M, Voříšková K, Mehedi Hasan Fuad M, Vetešník L, Šimková A
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Submission date Jan 23, 2024
Last update date May 17, 2024
Contact name Andrea Vetešníková Šimková
E-mail(s) simkova@sci.muni.cz
Organization name Masaryk University
Department Department of Botany and Zoology
Lab Parasitology
Street address Kamenice 5
City Brno
ZIP/Postal code 62500
Country Czech Republic
 
Platforms (3)
GPL25715 HiSeq X Ten (Cyprinus carpio)
GPL34122 HiSeq X Ten (Carassius gibelio)
GPL34123 HiSeq X Ten (Carassius auratus)
Samples (38)
GSM8031752 C. gibelio, diploid, female, replicate_1
GSM8031753 C. gibelio, diploid, female, replicate_2
GSM8031754 C. gibelio, diploid, female, replicate_3
Relations
BioProject PRJNA1068107

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE254010_DESeq2_Cg_3n_f_vs_Ca_2n_f.tsv.gz 5.2 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Ca_2n_m.tsv.gz 5.7 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Cc_2n_f.tsv.gz 4.7 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Cc_2n_m.tsv.gz 5.1 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Cg_2n_f.tsv.gz 4.6 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Cg_2n_m.tsv.gz 5.7 Mb (ftp)(http) TSV
GSE254010_DESeq2_Cg_3n_f_vs_Cg_3n_m.tsv.gz 5.8 Mb (ftp)(http) TSV
GSE254010_GO_BP_overrepresentation_David.txt.gz 1.0 Kb (ftp)(http) TXT
GSE254010_GO_CC_overrepresentation_David.txt.gz 785 b (ftp)(http) TXT
GSE254010_GO_MF_overrepresentation_David.txt.gz 1.7 Kb (ftp)(http) TXT
GSE254010_KEGG_overrepresentation_analysis.txt.gz 1.7 Kb (ftp)(http) TXT
GSE254010_all_probable_SNP_list.tsv.gz 5.2 Mb (ftp)(http) TSV
GSE254010_complete.feature_count.tsv.gz 8.4 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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