Aquatic plants
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736183 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14765185.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:estimating aquatic plant diversity using eDNA analyses Raw sequence reads
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Project description:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.
2023-12-12 | GSE238134 | GEO
Project description:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.
2023-12-12 | GSE238131 | GEO
Project description:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.
2023-12-12 | GSE238135 | GEO
Project description:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.
2023-12-12 | GSE238132 | GEO
Project description:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants, with a drastically reduced morphology and predominant clonal reproductive habit capable of continuous exponential growth. Here, we present assemblies of 10 Lemna chromosome sets by single molecule nanopore sequencing and chromosome conformation capture. Dynamics of genome evolution in the family are revealed by syntenic comparisons with Wolffia and Spirodela, and diversification of these genera was found to coincide with the “Azolla event”, in which blooms of aquatic macrophytes reduced atmospheric CO2 from greenhouse levels found in the Eocene to those of the current ice age. Orthologous gene comparisons with other aquatic and terrestrial plants uncovered candidate genes for the unique metabolic and developmental features of the family, such as frequent hybrid polyploidy, lack of stomatal closure in high CO2, and accumulation of calcium oxalate, a promising candidate for carbon sequestration. Loss of a spermine-triggered gene network accounts for drastic reduction in stature and preferentially adaxial stomata, a feature of floating aquatic plants. Strikingly, Lemnaceae genomes have selectively lost some of the genes required for RNA interference, including Argonaute genes required for post-zygotic reproductive isolation (the triploid block) and reduced gamete formation. Triploid hybrids arise commonly among Lemna, presumably by hybridization with unreduced gametes, and we have found mutations in highly-conserved ZMM crossover pathway genes that could support polyploid meiosis. Rapid but stable clonal propagation makes Lemna an ideal platform for protein and starch micro-cropping, and for sequestration of dissolved nutrients and atmospheric CO2. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by our recent engineering of high-oil Lemna lines that out-perform with oil seed crops.
2023-12-12 | GSE238133 | GEO
Project description:Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces thermotolerance of crops in a sustainable manner. Microbiome diversity of wheat plants is positively influenced by SA187 in open field agriculture, indicating that beneficial microbes can be a powerful tool to enhance agriculture in open field agriculture.
2021-02-28 | GSE147553 | GEO
Project description:Fungal samples of three different plants from wetlands Metagenome
| PRJNA881951 | ENA
Project description:High ambient temperature regulated the plant systemic response to the beneficial endophytic fungus Serendipita indica. Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild type plants.
2022-02-26 | GSE197325 | GEO
Project description:Microbiome diversity of three manure-based small biogas plants
| PRJEB38916 | ENA