Ontology highlight
ABSTRACT:
PROVIDER: PRJNA647289 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12275512_1.fastq.gz | Fastqsanger.gz | |||
| SRR12275512_2.fastq.gz | Fastqsanger.gz | |||
| SRR12275513_1.fastq.gz | Fastqsanger.gz | |||
| SRR12275513_2.fastq.gz | Fastqsanger.gz | |||
| SRR12275514_1.fastq.gz | Fastqsanger.gz |
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Project description:The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.
2021-11-23 | GSE179702 | GEO
Project description:The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.
2021-11-23 | GSE179697 | GEO
Project description:In this work, we evaluated the genetic stabilization process, of the intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae x Saccharomyces kudriavzevii) hybrids obtained by different non-GMO techniques, under fermentative conditions. Large-scale transitions in genome size, detected by measuring total DNA content, and genome reorganizations in both nuclear and mitochondrial DNA, evidenced by changes in molecular markers, were observed during the experiments. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns among the derived stable colonies was observed for intraspecific hybrids, particularly for those obtained by rare-mating in which the total amount of initial DNA was larger. Finally, a representative intraspecific stable hybrid underwent a normal industrial process to obtain active dry yeast production as an important point at which inducing changes in genome composition was possible. No changes in hybrid genetic composition after this procedure were confirmed by comparative genome hybridization. According to our results, fermentation steps 2 and 5 –comprising between 30 and 50 generations- suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. This work aimed to develop and validate a fast genetic stabilization method for newly generated Saccharomyces hybrids under selective enological conditions. A comparison of the whole stabilization process in intra- and interspecific hybrids showing different ploidy levels, as a result of using different hybridization methodologies, was also made.
2015-03-30 | GSE46192 | GEO
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1). 24 sampes, 12 DNA samples from parents and hybrids, 12 RNA sample from leaf and flowers of hybrids
2011-07-26 | E-GEOD-29037 | biostudies-arrayexpress
Project description:Hybridization of diverged taxa often result in lethality or sterility. We previously described natural variation for postzygotic incompatibility in the cross of diploid Arabidopsis thaliana to Arabidopsis arenosa. Hybrid seed death in this system has a complex genetic basis, involving many non-additive interactions. While activation of AGAMOUS-LIKE genes (AGL) and Athila elements have been detected 5-8 days after pollination (DAP), the molecular basis of death remains mysterious. To address this problem, we compared 3DAP transcriptomes in interspecific hybrids from two A. thaliana ecotypes, one compatible, the other incompatible. Relative to self crosses of the respective A. thaliana seed parent, hybrids displayed differential expression of key developmental regulators in both the endosperm and maternal seed coat as well as natural variation for stress response genes. Ribosomal protein genes and a photosynthetic cluster of genes were hyperactivated, presumably in response to growth signals. Suppressing endosperm growth factor IKU1 and defense response regulators such as NON-EXPRESSOR OF PATHOGENESIS RELATED1 (NPR1) improved hybrid seed survival. Therefore, in incompatible hybrids disruption of seed development most likely initiates in the endosperm, rapidly affecting embryo and seed coat. The activation of putative POLYCOMB REPRESSIVE COMPLEX (PRC) gene targets, together with a twenty-fold reduction in expression of the FERTILIZATION INDEPENDENT SEED 2 gene, indicates a PRC role. Examination of differential gene expression of incompatible A. thaliana eco. Col-0 X A. arenosa and compatible A. thaliana eco. C24 X A. arenosa hybrid seeds plus corresponding A. thaliana and A. arenosa control crosses.
2013-06-05 | E-GEOD-42957 | biostudies-arrayexpress
Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation.
2013-11-29 | GSE50049 | GEO
Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).
2011-07-27 | GSE29037 | GEO
Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation. Two biological replicate libraries sequenced from ribosome protected fragments as well as poly-A-selected mRNA of hybrids in addition to one biological replicate library of poly-A selected mRNA from each parental strain.
2013-11-29 | E-GEOD-50049 | biostudies-arrayexpress
Project description:Interspecific hybrids in Arabidopsis result in seed abortion that causes reproductive barrier. To investigate the allelic expression pattern at transcriptome level during early seed abortion stage, we performed RNA-seq analysis in F1 interspecific hybrids with three different ecotypes in A. thaliana as maternal and A. arenosa as paternal and identified MEGs and PEGs. Interestingly, PEGs showed distinct expression pattern in several aspects, compared to MEGs: PEGs showed ecotype-specific expression pattern, suggesting a role for PEGs in ecotype-dependent seed lethality. 35% of previously known MEGs in non-lethal hybrids were found as PEGs in our lethal interspecific hybrids, implying the presence of abnormal paternal allelic upregulation. The correlation test between the upregulation of PEGs and previously reported paternal-excess interploidy cross (2X6) which exhibited seed abortion showed that dosage disruption by abnormal paternal upregulation is correlated with seed abortion. Moreover, epigenetic disruption appears to cause some of abnormal upregulation of paternal alleles in PEGs via mis-regulation of MEA-mediated PcG2 and MET1-mediated DNA methylation. The results provide clue on the critical role of PEGs in seed abortion via disruption of dosage balance and epigenetic regulation.
2015-10-01 | GSE41391 | GEO
Project description:In this work, we evaluated the genetic stabilization process, of the intra- (Saccharomyces cerevisiae) and interspecific (S. cerevisiae x Saccharomyces kudriavzevii) hybrids obtained by different non-GMO techniques, under fermentative conditions. Large-scale transitions in genome size, detected by measuring total DNA content, and genome reorganizations in both nuclear and mitochondrial DNA, evidenced by changes in molecular markers, were observed during the experiments. Interspecific hybrids seem to need fewer generations to reach genetic stability than intraspecific hybrids. The largest number of molecular patterns among the derived stable colonies was observed for intraspecific hybrids, particularly for those obtained by rare-mating in which the total amount of initial DNA was larger. Finally, a representative intraspecific stable hybrid underwent a normal industrial process to obtain active dry yeast production as an important point at which inducing changes in genome composition was possible. No changes in hybrid genetic composition after this procedure were confirmed by comparative genome hybridization. According to our results, fermentation steps 2 and 5 –comprising between 30 and 50 generations- suffice to obtain genetically stable interspecific and intraspecific hybrids, respectively. This work aimed to develop and validate a fast genetic stabilization method for newly generated Saccharomyces hybrids under selective enological conditions. A comparison of the whole stabilization process in intra- and interspecific hybrids showing different ploidy levels, as a result of using different hybridization methodologies, was also made. A stable hybrid strain was compared with itself before and after ADY (active dry yeast) production in order to evaluate the genetic stability of this strain.
2015-03-30 | E-GEOD-46192 | biostudies-arrayexpress