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Rice paddy metagenome

ABSTRACT: Bacterial diversity of surface soil with different distances away from a drainage ditch in a cold waterlogged paddy field.

PROVIDER: PRJNA300325 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR2954700_1.fastq.gz	Fastqsanger.gz
	SRR2954700_2.fastq.gz	Fastqsanger.gz
	SRR2954702_1.fastq.gz	Fastqsanger.gz
	SRR2954702_2.fastq.gz	Fastqsanger.gz
	SRR2954693_1.fastq.gz	Fastqsanger.gz

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soil metagenome

Project description:Fungal diversity of surface soil with different distances away from a drainage ditch in a cold waterlogged paddy field.

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A blueprint for C4 photosynthesis in the rice paddy: insights from the noxious weed Echinochloa glabrescens

Project description:The C4 pathway is a highly complex trait that increases photosynthetic efficiency in over sixty plant lineages. Although the majority of C4 plants occupy disturbed, arid and nutrient-poor habitats, some grow in high-nutrient, waterlogged conditions. One such example is Echinochloa glabrescens, which is an aggressive weed of rice paddies. We generated comprehensive transcriptome datasets for C4 E. glabrescens and C3 rice to identify genes associated with adaption to waterlogged, nutrient-replete conditions, but also used the data to better understand how C4 photosynthesis operates in these conditions. Similar to arid C4 species, leaves of E. glabrescens exhibited classical Kranz anatomy with lightly lobed mesophyll cells. As with rice and other hygrophytic C3 species, leaves of E. glabrescens accumulated a chloroplastic phosphoenolpyruvate carboxylase protein, albeit at reduced levels relative to rice. We identified a molecular signature associated with C4 photosynthesis in nutrient-replete, waterlogged conditions that is highly similar to those previously reported from C4 plants that grow in more arid conditions. We also identified a cohort of genes that have been subjected to a selective sweep associated with growth in paddy conditions. Overall, this approach highlights the value of using wild species such as weeds to identify adaptions to specific conditions associated with high-yielding crops in agriculture.

2015-08-11 | E-MTAB-4422 | biostudies-arrayexpress

Gene expression profile of leaf in rice grown under paddy field with macronutrient deficiencies

Project description:Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice leaves under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions in paddy field to obtain a global view of gene regulations associated with plant response to essential nutrients.

2019-10-06 | GSE73766 | GEO

Rice root response atlas

Project description:Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.

2022-05-02 | GSE180100 | GEO

rice paddy metagenome

Project description:Soil microbial communities in a lowland paddy rice field in Central Kenya

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Rice paddy

Project description:Rice paddy Metagenome

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rice paddy metagenome

Project description:Enhanced electricity generation in rice paddy-field microbial fuel cells supplemented with iron powders

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rice paddy metagenome

Project description:Amplicon sequencing analysis of bacterial 16S rRNA gene in a iron-toxic paddy field

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Bacillus altitudinis strain:paddy field | isolate:paddy field

Project description:Bacillus altitudinis strain:paddy field | isolate:paddy field Genome sequencing

| PRJNA1077217 | ENA

Diurnal variation for rice leaves in Toyama field in 2012

Project description:We have previously demonstrated statistical modeling of gene expression under various environmental factors using field transcriptome data obtained from samples grown in a paddy field at Tsukuba, Japan. In this series of experiments, we would like to improve the models for practical use. In order to do that, we have done field transcriptome assay in seven paddy fields at different sites in Japan (or, Sappro, Furukawa, Toyama, Tsukuba, Takatsuki, Furukawa, and Fukuoka). This data is from one of the places, Toyama.

2017-03-31 | GSE65598 | GEO

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