Ontology highlight
ABSTRACT:
PROVIDER: PRJNA575642 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10224432_1.fastq.gz | Fastqsanger.gz | |||
| SRR10224432_2.fastq.gz | Fastqsanger.gz | |||
| SRR10224433_1.fastq.gz | Fastqsanger.gz | |||
| SRR10224433_2.fastq.gz | Fastqsanger.gz | |||
| SRR10224434_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.
2010-11-10 | E-GEOD-18961 | biostudies-arrayexpress
Project description:Our recently published results demonstrated a crucial role for plastid terminal oxidase (PTOX) as an alternative electron pathway in the halophyte Spartina alterniflora (S. alterniflora) under salt stress but not for the glycophyte Setaria viridis (S. viridis). Herein, the effect of salt on the photosynthetic electron transport and RNA-seq analysis was probed in Setaria and its salt-tolerant close relative S. alterniflora. Initially, plants were grown at soil then were salt-treated under hydroponic conditions for two weeks. Setaria shows high vulnerability to salt compared to Spartina; while, Setaria was unable to survive exposure to greater than 100 mM, Spartina could tolerate salt concentrations as high as 550 mM with merely negligible effect on gas exchange and conductance of electrons transport chain (gETC). After exposure to salt, the prompt fluorescence (OJIP-curves) reveals an increase in the O- and J-steps in Setaria and very less or no change for SA. This suggests a higher QA over-reduction in Setaria than in Spartina. Following salt treatment, a dramatic decline in PSII primary photochemistry for Setaria was observed, as displayed by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII. However, no substantial change was recorded regarding these parameters for Spartina under NaCl treatment. Interestingly, we report an improvement in primary PSII photochemistry (ΦPSII) for Spartina with increasing either salt concentration or duration. Besides, the magnitude of NPQ dynamics was strongly enhanced for Setaria even at low NaCl level (50 mM); however, it remains unchangeable or slightly increased for Spartina at high NaCl concentrations (above 400 mM). For plants endured salt, we notice an increase in both the proportion of oxidized P700 and the amount of active P700 in Setaria and almost no change for Spartina. The slowdown of electrons flow through PSII was accompanied by a dramatic decline in gETC. Under salt, CO2 assimilation (A) and stomatal conductance (gs) evaluations demonstrate that A decreases earlier, even after one week exposure to only 50 mM NaCl for Setaria; however, the effect of salt was negligible in Spartina regarding these two parameters even after exposure for two weeks to high salt levels (400 and 550 mM). For Setaria exposed for 12 d to salt, the use of 2,000 μmol m-2 s-1 external CO2 was not sufficient to fully restore A to the control level as assessed by A-Ci curves, even for 50 mM salt. The A at all NaCl levels, except 550 mM, was able to completely recover to initial level before stress in Spartina. RNAseq analysis shows a stimulation of oxido-reduction reactions in Setaria. Gene onthology (GO) enrichment emphasizes differentially expressed genes (DEGs) and some transcription factors (TFs) under salt. The up-regulated genes in Setaria are related to three metabolic processes; C4, photorespiration and the oxidation/reduction pathways. Some other specifically highly up-regulated genes in Setaria are mostly related to TFs including DNA-binding transcription factor activity, stress marker genes such as peroxidase and senescence-related genes such as flavonol synthase.
2022-03-09 | GSE146718 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids.
2010-11-10 | GSE18961 | 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:The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants was a major evolutionary event that has transformed our planet. So far lack of genome information on unicellular charophyte algae hinders our understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.
2019-11-21 | GSE123851 | GEO