Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA115805 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to M-bM-^@M-^\genomic shockM-bM-^@M-^], whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development. NOTE: sff files unavailable for Samples AaL and F1L. 10 samples examined: Arabidopsis thaliana leaf, flower, Arabidopsis arenosa leaf and flower, F1 synthetic allopolyploid leaf and flower, F7 synthetic allopolyploid leaf and flower, Arabidopsis suecica leaf and flower. To determine small RNA profiles in Arabidopsis allotetraploids and their progenitors, we made 10 small RNA libraries from rosette leaves (L) and flower buds (F) in five lines, A. thaliana, A. arenosa, Allo(F1), Allo733(F7), and A. suecica. To examine expression of small RNAs among related species and their hybrids, we employed miRNA microarrays and compared small RNA levels.
2009-07-30 | E-GEOD-15443 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to “genomic shock”, whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development. NOTE: sff files unavailable for Samples AaL and F1L.
2009-07-31 | GSE15443 | GEO
Project description:Small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs), control gene expression and epigenetic regulation. Although the roles of miRNAs and siRNAs have been extensively studied, their expression diversity and evolution in closely related species and interspecific hybrids are poorly understood. Here, we show comprehensive analyses of miRNA expression and siRNA distributions in two closely related species Arabidopsis thaliana and Arabidopsis arenosa, a natural allotetraploid Arabidopsis suecica, and two resynthesized allotetraploid lines (F(1) and F(7)) derived from A. thaliana and A. arenosa. We found that repeat- and transposon-associated siRNAs were highly divergent between A. thaliana and A. arenosa. A. thaliana siRNA populations underwent rapid changes in F(1) but were stably maintained in F(7) and A. suecica. The correlation between siRNAs and nonadditive gene expression in allopolyploids is insignificant. In contrast, miRNA and tasiRNA sequences were conserved between species, but their expression patterns were highly variable between the allotetraploids and their progenitors. Many miRNAs tested were nonadditively expressed (deviating from the mid-parent value, MPV) in the allotetraploids and triggered unequal degradation of A. thaliana or A. arenosa targets. The data suggest that small RNAs produced during interspecific hybridization or polyploidization serve as a buffer against the genomic shock in interspecific hybrids and allopolyploids: Stable inheritance of repeat-associated siRNAs maintains chromatin and genome stability, whereas expression variation of miRNAs leads to changes in gene expression, growth vigor, and adaptation.
| S-EPMC2757398 | biostudies-literature
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: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
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:Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2nâ=â2xâ=â24, genome AA) and the tetraploid form of O. punctata (2nâ=â4xâ=â48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico âhybridsâ (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.
2015-05-02 | E-MTAB-4225 | biostudies-arrayexpress
Project description:Hybrid progeny can enjoy increased fitness and stress tolerance relative to their ancestral species, a phenomenon known as hybrid vigor. Though this phenomenon has been documented throughout the Eukarya, evolution of hybrid populations has yet to be explored experimentally in the lab. To fill this knowledge gap we created a pool of Saccharomyces cerevisiae and S. bayanus homoploid and aneuploid hybrids, and then investigated how selection in the form of incrementally increased temperature or ethanol impacted hybrid genome structure and adaptation. During 500 generations of continuous ammonia-limited, glucose-sufficient culture, temperature was raised from 25C to 46??C. This selection invariably resulted in nearly-complete loss of the S. bayanus genome, although the dynamics of genome loss differed among independent replicates. Temperature-evolved isolates were significantly more thermal tolerant and exhibited greater phenotypic plasticity than parental species and founding hybrids. By contrast, when the same hybrid pool was subjected to increases in exogenous ethanol from 0% to 14%, selection favored euploid S. cerevisiae x S. bayanus hybrids. Ethanol-evolved isolates exhibited significantly greater ethanol tolerance relative only to S. bayanus and one of the founding hybrids tested. Adaptation to thermal and ethanol stress manifested as heritable changes in cell wall structure demonstrated by resistance to zymolyase or micafungin treatment. This is the first study to show experimentally that the fate of interspecific hybrids critically depends on the type of selection they encounter during the course of evolution.
2012-08-01 | GSE24479 | GEO
Project description:Hybrid progeny can enjoy increased fitness and stress tolerance relative to their ancestral species, a phenomenon known as hybrid vigor. Though this phenomenon has been documented throughout the Eukarya, evolution of hybrid populations has yet to be explored experimentally in the lab. To fill this knowledge gap we created a pool of Saccharomyces cerevisiae and S. bayanus homoploid and aneuploid hybrids, and then investigated how selection in the form of incrementally increased temperature or ethanol impacted hybrid genome structure and adaptation. During 500 generations of continuous ammonia-limited, glucose-sufficient culture, temperature was raised from 25C to 46??C. This selection invariably resulted in nearly-complete loss of the S. bayanus genome, although the dynamics of genome loss differed among independent replicates. Temperature-evolved isolates were significantly more thermal tolerant and exhibited greater phenotypic plasticity than parental species and founding hybrids. By contrast, when the same hybrid pool was subjected to increases in exogenous ethanol from 0% to 14%, selection favored euploid S. cerevisiae x S. bayanus hybrids. Ethanol-evolved isolates exhibited significantly greater ethanol tolerance relative only to S. bayanus and one of the founding hybrids tested. Adaptation to thermal and ethanol stress manifested as heritable changes in cell wall structure demonstrated by resistance to zymolyase or micafungin treatment. This is the first study to show experimentally that the fate of interspecific hybrids critically depends on the type of selection they encounter during the course of evolution. Array-CGH was performed on the S. cerevisiae parent strain CEN.PK (GSY2160), the S. bayanus parent strain CBS7001 (GSY2161) and on the F1 interspecific hybrid resulting from mating the 2 parents (GSY2168). Additionally, three rare viable spores obtained after sporulation of the F1 were assayed by array-CGH (F2a, F2b, F2c). A large pool of F2 spores (and probably some number of F1 hybrid cells) were subjected to gradually increasing temperatures, in three independent vessels, with populations sampled at various generation times. Likewise, the same pool was used to found populations in an additional three independent vessels, which were then subjected to gradually increasing ethanol concentrations (at constant temperature). Array-CGH was performed on three different clones from each of the three temperature vessels at the final 500 generation time point (T500 clones). Biological replicates of the T500 clones were performed (T500-new). Two self-self array-CGH hybridization controls were also performed (self-control). Array-CGH was performed on one clone from each of the three ethanol vessels taken at the 400 generation timepoint (EtOH400gen clones).
2012-07-31 | E-GEOD-24479 | biostudies-arrayexpress
Project description:Evolution of S. cerevisiae - S. bayanus Interspecific Hybrids
| PRJNA132509 | ENA