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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

ABSTRACT: Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

PROVIDER: PRJNA343173 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4250010_1.fastq.gz	Fastqsanger.gz
	SRR4250010_2.fastq.gz	Fastqsanger.gz
	SRR4250011_1.fastq.gz	Fastqsanger.gz
	SRR4250011_2.fastq.gz	Fastqsanger.gz
	SRR4250012.fastq.gz	Fastqsanger.gz

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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

2018-03-01 | GSE86979 | GEO

Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [RNA-Seq]

2018-03-01 | GSE86991 | GEO

Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

Project description:Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [WGBS]

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Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-03-01 | GSE86992 | GEO

RNA-protein dynamics of high CO2-adapted, iron-phosphorus co-limited Trichodesmium reveals nutrient-limited molecular architecture of a globally significant marine nitrogen fixer in a future ocean

Project description:Our paper presents the results of a study in which we used Illumina RNA-Seq (i.e. transcriptomics) and high-CO2 nutrient limitation experiments to examine transcriptional variation of iron-limited, phosphorus-limited, and iron-phosphorus co-limited cultures following long-term (~7 years) low- (380 µatm CO2) and high-CO2 (750 µatm CO2) selection. Hence, we describe the molecular physiology of the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

2017-10-23 | GSE94951 | GEO

Trichodesmium erythraeum IMS101

Project description:Biogeographic conservation and CO2-dynamics of the cytosine methylome in the globally important cyanobacterium Trichodesmium [RNA-Seq]

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Long-term epigenomic modifications underlying trait canalization to high CO2 in the biogeochemically-important marine cyanobacterium Trichodesmium [WGBS]

Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors.

2020-08-18 | GSE138174 | GEO

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Project description:The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.

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Project description:We present population-level epigenetic variation in Trichodesmium erythraeum IMS101 associated with steady-state Fe-limitation at two different P concentrations on both short (i.e. 2 months) and long timescales (i.e. ~1 year).

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