Ontology highlight
ABSTRACT:
PROVIDER: PRJNA360668 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5161760.fastq.gz | Fastqsanger.gz | |||
| SRR5161761.fastq.gz | Fastqsanger.gz | |||
| SRR5161762.fastq.gz | Fastqsanger.gz | |||
| SRR5161763.fastq.gz | Fastqsanger.gz | |||
| SRR5161764.fastq.gz | Fastqsanger.gz |
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Project description:Centromeric repetitive DNA sequences are highly variable during evolution, which are the hub for genome stability in almost all the eukaryotic organisms. However, how centromeric repeat sequences diverge rapidly among closely related species and populations, and how polyploidy contributed to the diversity of centromere among co-evolved subgenomes are largely unknown. Here, we applied the Brachypodium system to investigate the track of centromere evolution within this taxa, and their adaptation to alloploidization process. Subgenome divergent centromeric satellite repeat were discovered in tetraploid B. hybridum, and this divergent was originated form their two diploid progenitors. Furthermore, differential sequences influence the association sites with CENH3 nucleosomes on the monomer satellite repeats, and positioning of CENH3 nucleosomes on the satellite DNA are stable in each subgenome after alloploidization. Only minor intrasubgenomic variations were observed on these satellite repeats from diploid to tetraploid in B. hybridum, and no evident intersubgenomic transfer of centromeric satellite repeats after alloploidization. Pan-genome analysis reveals that the general principle of centromere dynamic within the populations in Brachypodium genomes with different polyploidy level. Our results provide an unprecedented information regarding the genomic and functional diversity of centromeric repeat DNA during evolution.
2022-12-01 | GSE157143 | GEO
Project description:Microarray analysis on Brachypodium distachyon seedlings was performed to determine the response of the transcriptome to changes in ambient temperature, including identification of marker genes that were up-regulated or down-regulated by a moderate increase in growth temperature. Wild-type Brachypodium (Bd21) seedlings were grown on MSR63 media without sucrose (Alves et al. 2009 Nature Protocols vol. 4 pp 638-649) in a short-day photoperiod (14 hr light/ 10 hr dark) at 17 ºC. As the third leaf was emerging, plants were transferred to 12 ºC for 48 hrs. Plants were then maintained at 12 ºC or transferred to one of two temperature treatments: constant 22 ºC or constant 27 ºC. Samples were collected before the shift (0 hr) and at 2 hr and 24 hr after the shift and immediately frozen in liquid nitrogen. For each harvest, two to three replicates were collected that each contained 3 seedlings.
2013-06-07 | E-MEXP-3918 | biostudies-arrayexpress
Project description:We conducted two iron-temperature bioassay incubation experiments during the austral summer of 2018-2019 in the Weddell Sea, Southern Ocean. The first bioassay (BA1) was initiated on December 28th, 2018, approximately 560 km away from the ice edge at 65°S 0.038°E. The second bioassay (BA2) was initiated on January 9th, 2019, approximately 70 km from the ice edge at 70.15°S 11.02°W (Figure 1A). For both bioassays, we collected sea water at 20 m depth using a custom-built ultraclean CTD sampling system – “Titan” (De Baar et al. 2008). We chose this depth to minimize light shock when the microbial community was brought on deck, and to prevent trace metal contamination from the ship. After recovery, Titan was moved into a dedicated, temperature-controlled, trace-metal-clean (TMC) laboratory container where the sea water was used for initial (T0) sampling, and to fill triplicate, 20 L, TMC cubitainers for each iron-temperature treatment. The treatment matrix including four iron-temperature conditions: low iron – low temperature, high iron – low temperature, low iron – high temperature, high iron – high temperature. We did not add any iron to the low iron treatments. We supplemented the high iron treatments with a naturally occurring but rare isotope of 57Fe, which allowed us to differentiate between the added iron and iron already present in the water (mainly 56Fe). For this, we made a 40 µM 57FeCl3 stock solution in 0.1 M trace-metal grade HCl, then added 1 mL of this stock to each of the high iron cubitainers. This resulted in an initial dissolved 57Fe concentration of 2 nM in the high iron treatments. We then sealed the cubitainers and placed them inside temperature-controlled deck incubators where the low temperature treatments were incubated under in situ temperature, and the high temperature treatments were incubated under in situ + 2 °C (Table S1).
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Project description:Several reports have investigated the effects of future climate conditions on photosynthesis and biomass production in woody plants but none combining temperature and atmospheric CO2 concentration. We used grow chambers to expose Eucalyptus grandis and E. globulus seedlings to three temperature regimes (10-12°C - low temperature, 20-22°C - control temperature and 33-35°C - high temperature) combined with two CO2 concentration (390 ppm – normal and 700 ppm - high). After 35 days the stems were used for transcriptome (RNAseq) analysis aiming to understand changes in the expression of genes related with biosynthesis and remodeling of the cell wall, as well as genes related with carbon partitioning and hormonal regulation. E. globulus, a species adapted to low temperature, was more responsive to the treatments compared to E. grandis. The most relevant biological processes affected by the treatments were related to stress, secondary metabolism, hormonal response, and signaling. We also analyzed in depth all cell wall biopolymer synthetic genes and their regulation by innumerous transcriptional factors. There was an upregulation of ethylene and auxin biosynthetic genes in both species, but it was stronger under high and low temperature in E.globulus. Temperature was more effective to change cell wall biosynthetic genes than CO2 and CO2 stimulated lignin biosynthetic pathway. We also analyzed lignin composition and structure. There was an increase in F5H and COMT expression and the S/G ratio also increased under high CO2 in E.globulus. Thus, the species responded differently to treatments and stem composition and development was highly affected by temperature and CO2 concentration.
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Project description:Temperature is a critical environmental factor governing plant growth and development. The difference between day temperature (DT) and night temperature (NT), abbreviated as DIF, influences plant architecture. Subjecting plants to artificial DIF treatments is an effective strategy in ornamental horticulture. For example, negative DIF (when DT – NT < 0) generally inhibits stem elongation, resulting in dwarf plants. However, the mechanisms underlying stem growth regulation by DIF remains to be completely elucidated. In this study, we aimed to analyze the growth, transcriptome, and phytohormone profiles of tomato (Solanum lycopersicum) seedlings grown under different DIF treatments. Under positive DIF (when DT – NT > 0), in contrast to the control temperature (25°C/20°C, DT/NT), high temperature (30°C/25°C) increased stem length and thickness, as well as the number of xylem vessels. Conversely, compared with the positive high temperature DIF treatment (30°C/25°C), under negative DIF treatment (25°C/30°C) stem elongation was inhibited, but stem thickness and the number of xylem vessels were not affected. The negative DIF treatment decreased the expression of gibberellin (GA)-, auxin-, and cell wall-related genes in the epicotyl, as well as the concentrations of GAs and indole-3-acetic acid (IAA). The expression of these genes and concentrations of these hormones increased under high temperature compared to those under the control temperature positive DIF. Our results suggest that stem length in tomato seedlings is controlled by changes in GA and IAA biosynthesis in response to varying day and night temperatures.
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Project description:For identification of genes up-regulated in abiotic stress (drought, high salinity, low temperature and ABA) treated rice, total RNA (100 μg) was prepared from root tissues of 14-d-old rice seedlings (Oryza sativa cv Nakdong) grown under normal growth conditions. For the high salinity and ABA treatments, the 14-d-old seedlings were transferred to a nutrient solution containing 400 mM NaCl or 100 μM ABA for 2 h in the greenhouse under continuous light of approximately 1000 μmol m-2 s -1. For drought treatment, 14-d-old seedlings were air-dried for 2 h also under continuous light of approximately 1000 μmol m-2 s -1. For low temperature treatments, 14-d-old seedlings were exposed at 4°C in a cold chamber for 6 h under continuous light of 150 μmol m-2 s -1.
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