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Incomplete reprogramming of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

ABSTRACT: Incomplete reprogramming of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

PROVIDER: PRJEB26932 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2596710_1.fastq.gz	Fastqsanger.gz
	ERR2596710_2.fastq.gz	Fastqsanger.gz
	ERR2596720_1.fastq.gz	Fastqsanger.gz
	ERR2596720_2.fastq.gz	Fastqsanger.gz
	ERR2596730_1.fastq.gz	Fastqsanger.gz

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Project description: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.

Project description:Symbiotic microorganisms play an important role in the growth and development of marine invertebrates, such as the sea moon, affecting their metamorphosis process. The outbreak of jellyfish puts pressure on marine ecosystems and affects their stability. However, researches on the development of jellyfish are still fewer, the use of biological control of jellyfish disaster is still in the theoretical stage, and the inhibition mechanism of microorganisms on jellyfish remains to be revealed. We isolated a strain of Bacillus paramycoides SG15 from rhizosphere sediments of seagrass Zostera japonica, and found that this strain could inhibit the asexual reproduction of jellyfish Aurelia coerulea polyp larva. Through co-culture experiments, we used transcriptomics, metabolomics and fluorescence in situ hybridization techniques, combined with the genome and metabolome of SG15, and found that this isolate could inhibit the asexual reproduction rate of the larva polyp by inhibiting the absorption of vitamins, and the endoderm cells were the most important action site of SG15. Although there are relatively high concentrations of vitamins and their derivatives in the surrounding environment, the transport of hydra is reduced, and most vitamins cannot be synthesized in the polys as well, thus affecting the growth and reproduction of polyps. Our study, analyzed the interaction processes between Bacillus and polyps and revealed the inhibiting mechanism of the polyp asexual reproduction by B. paramycoides SG15, which laid a theoretical foundation for the subsequent analysis of interactions between jellyfish and microorganisms, bring materials for the biological control of jellyfish disasters. Polyps culture media is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9419' rel='noopener noreferrer' target='_blank'>MTBLS9419</a>.Polyps whole organism is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9409' rel='noopener noreferrer' target='_blank'>MTBLS9409</a>.

Project description:Symbiotic microorganisms play an important role in the growth and development of marine invertebrates, such as the sea moon, affecting their metamorphosis process. The outbreak of jellyfish puts pressure on marine ecosystems and affects their stability. However, researches on the development of jellyfish are still fewer, the use of biological control of jellyfish disaster is still in the theoretical stage, and the inhibition mechanism of microorganisms on jellyfish remains to be revealed. We isolated a strain of Bacillus paramycoides SG15 from rhizosphere sediments of seagrass Zostera japonica, and found that this strain could inhibit the asexual reproduction of jellyfish Aurelia coerulea polyp larva. Through co-culture experiments, we used transcriptomics, metabolomics and fluorescence in situ hybridization techniques, combined with the genome and metabolome of SG15, and found that this isolate could inhibit the asexual reproduction rate of the larva polyp by inhibiting the absorption of vitamins, and the endoderm cells were the most important action site of SG15. Although there are relatively high concentrations of vitamins and their derivatives in the surrounding environment, the transport of hydra is reduced, and most vitamins cannot be synthesized in the polys as well, thus affecting the growth and reproduction of polyps. Our study, analyzed the interaction processes between Bacillus and polyps and revealed the inhibiting mechanism of the polyp asexual reproduction by B. paramycoides SG15, which laid a theoretical foundation for the subsequent analysis of interactions between jellyfish and microorganisms, bring materials for the biological control of jellyfish disasters. Polyps whole organism is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS9409' rel='noopener noreferrer' target='_blank'>MTBLS9409</a>.Polyps culture media is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS9419' rel='noopener noreferrer' target='_blank'>MTBLS9419</a>.

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Incomplete reprogramming of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation

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