Asteraceae species
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ABSTRACT:
PROVIDER: PRJNA764566 | ENA |
REPOSITORIES: ENA
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Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species.
2015-01-08 | GSE54339 | GEO
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress
Project description:Induction of DNA double-strand breaks (DSBs) in ribosomal DNA (rDNA) repeats is associated with ATM-dependent repression of ribosomal RNA synthesis and large-scale reorganization of nucleolar architecture, but the signaling events that regulate these responses are largely elusive. Here we show that the nucleolar response to rDNA breaks is dependent on both ATM and ATR activity. We further demonstrate that ATM- and NBS1-dependent recruitment of TOPBP1 in the nucleoli is required for inhibition of ribosomal RNA synthesis and nucleolar segregation in response to rDNA breaks. Mechanistically, TOPBP1 recruitment is mediated by phosphorylation-dependent interactions between three of its BRCT domains and conserved phosphorylated Ser/Thr residues at the C-terminus of the nucleolar phosphoprotein Treacle. Our data thus reveal an important cooperation between TOPBP1 and Treacle in the signaling cascade that triggers transcriptional inhibition and nucleolar segregation in response to rDNA breaks.
2019-12-06 | PXD015138 | Pride
Project description:The ability of environmental exposures in one generation to elicit phenotypic outcomes in subsequent generations suggests that DNA is not the sole vehicle of biological heredity. Such non-genetic inheritance has been demonstrated in a variety of non-mammalian species but, to date, has remained controversial and inadequately characterised in mammals. Here, we show that early life protein restriction (PR) in mice alters DNA methylation at specific genetic variants of multi-copy ribosomal DNA (rDNA), to produce a linear correlation with the extent of growth restriction induced by PR. These effects are common to soma and germ-line and are concomitant with changes in the relative abundance of the responsive rDNA genetic variant. Intergenerational pedigree analysis reveals that rDNA genetic correlations are abolished between directly exposed males and their unexposed offspring, and epigenetic correlations are gained. To the best of our knowledge, this is the first direct demonstration in mammals of epigenetic dynamics induced by gene-environment interactions. Our work confirms rDNA as an evolutionarily conserved target of nutritional insults and intergenerational effects in flies, yeast, and now mice.
2016-07-08 | GSE72609 | GEO
Project description:The ability of environmental exposures in one generation to elicit phenotypic outcomes in subsequent generations suggests that DNA is not the sole vehicle of biological heredity. Such non-genetic inheritance has been demonstrated in a variety of non-mammalian species but, to date, has remained controversial and inadequately characterised in mammals. Here, we show that early life protein restriction (PR) in mice alters DNA methylation at specific genetic variants of multi-copy ribosomal DNA (rDNA), to produce a linear correlation with the extent of growth restriction induced by PR. These effects are common to soma and germ-line and are concomitant with changes in the relative abundance of the responsive rDNA genetic variant. Intergenerational pedigree analysis reveals that rDNA genetic correlations are abolished between directly exposed males and their unexposed offspring, and epigenetic correlations are gained. To the best of our knowledge, this is the first direct demonstration in mammals of epigenetic dynamics induced by gene-environment interactions. Our work confirms rDNA as an evolutionarily conserved target of nutritional insults and intergenerational effects in flies, yeast, and now mice.
2016-07-08 | GSE72608 | GEO
Project description:The ability of environmental exposures in one generation to elicit phenotypic outcomes in subsequent generations suggests that DNA is not the sole vehicle of biological heredity. Such non-genetic inheritance has been demonstrated in a variety of non-mammalian species but, to date, has remained controversial and inadequately characterised in mammals. Here, we show that early life protein restriction (PR) in mice alters DNA methylation at specific genetic variants of multi-copy ribosomal DNA (rDNA), to produce a linear correlation with the extent of growth restriction induced by PR. These effects are common to soma and germ-line and are concomitant with changes in the relative abundance of the responsive rDNA genetic variant. Intergenerational pedigree analysis reveals that rDNA genetic correlations are abolished between directly exposed males and their unexposed offspring, and epigenetic correlations are gained. To the best of our knowledge, this is the first direct demonstration in mammals of epigenetic dynamics induced by gene-environment interactions. Our work confirms rDNA as an evolutionarily conserved target of nutritional insults and intergenerational effects in flies, yeast, and now mice.
2016-07-08 | GSE72607 | GEO
Project description:We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
2021-04-23 | GSE169088 | GEO
Project description:Ribosomal DNA (rDNA) arrays are highly repetitive regions of the genome which encode essential genes required to produce ribosomes. DNA double-stranded breaks (DSBs) generated within rDNA genes elicit a unique cellular response involving robust transcriptional silencing and nucleolar reorganization into ‘cap’ structures at the nucleolar periphery. This process is coordinated by the nucleolar scaffolding protein TCOF1, which functions to recruit the DNA repair proteins NBS1 and TOPBP1 that activate the ATM and ATR kinases, resulting in ribosomal RNA (rRNA) transcriptional silencing and nucleolar segregation. However, the DNA damage and repair response at rDNA arrays remains incompletely understood. Here, we investigate the cellular response to rDNA DSBs using proteomics and genetic CRISPR-Cas9 screening. We show that the protein UFMylation pathway and the HUSH complex are important for cell viability and survival in response to rDNA DSBs, and that the E3 UFM1-ligase UFL1 and its heterodimer DDRGK1 are associated with TCOF1 at nucleolar caps. Loss of UFL1 leads to impaired ATM activation, reduced rRNA transcriptional silencing, and an overall reduction in nucleolar segregation. We identified ATM, UNC45A and SMC6 as UFMylated proteins, in which UFMylation may facilitate ATM activation and segregation of damaged rDNA to the nucleolar periphery. Altogether, our findings provide the first evidence for a role for UFMylation in rDNA DSB repair.
2024-01-29 | GSE253809 | GEO
Project description:Ribosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. In Drosophila rDNA units damaged by insertions of retrotransposons are repressed by an unknown mechanism. Here, we established a new model to study regulation of rDNA expression using molecularly marked rDNA transgenes. Using this model, we show that insertion of any heterologous sequence into rDNA leads to transcriptional repression. We found that SUMO (Small Ubiquitin-like Modifier) is required for efficient repression of damaged rDNA units. Surprisingly, SUMO also controls expression of intact rDNA, demonstrating that a single pathway is responsible for both selective repression of damaged units and silencing of surplus rDNA.
2020-02-01 | GSE141068 | GEO
Project description:Eco1 is the acetyltransferase that establishes sister-chromatid cohesion during DNA replication. Budding yeast with an eco1 mutation that genocopies Roberts syndrome displaysreduced ribosomal DNA (rDNA) transcription and a transcriptional signature of starvation. Weshow that deleting FOB1, a gene encoding a specific replication fork blocking protein for therDNA region, rescues rRNA production and partially rescues transcription genome-wide. This experiment examines the effect of eco1 mutation on replication genome-wide. Furtherstudies show that deletion of FOB1 corrects the genome-wide replication defects, nucleolarstructure, and rDNA segregation in an eco1 mutant. Our study highlights cohesin's central role atthe rDNA for global control of DNA replication and gene expression. DNA content in eco1-W216G mutant and wt yeast is measured in duplicate by sequencing at 0, 20, and 40 minutes following release from G1 arrest.
2014-04-03 | E-GEOD-54742 | biostudies-arrayexpress