Aquatic plants
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736183 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14765185.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:estimating aquatic plant diversity using eDNA analyses Raw sequence reads
| PRJNA665275 | ENA
Project description:Chronic ionizing radiation imposes direct and indirect damage on plants that could modify their morphology, biochemistry, physiology, as well as responses to biotic agents. Plants experience elevated levels of DNA damage and reactive oxygen species; thus, they adjust cellular homeostasis. Aquatic ecosystems in Chornobyl zone, a major radiological disaster site, are contaminated by harmful radionuclides. This study focused on changes in the proteome of leaves as well as carbonylated proteins, which might explain the biochemical mechanisms responsible for the susceptibility of a wild aquatic plant (common reed, Phragmites australis) grown in Chornobyl zone to biotic stress. The fungal infection assay indicated that life in a radionuclide-contaminated environment compromised plant immunity. The protein profiling identified 1,867 proteins; among them, 174 were differentially accumulated. We selected several dozen proteins with consistently higher and lower abundance in the samples from areas around the contaminated lakes by hierarchical clustering. Discordant expression of coding genes pointed to posttranscriptional regulation. Furthermore, the quantification of antioxidant enzyme activities (glutathione reductase, ascorbate peroxidase, catalase, and glutathione S-transferase) and carbonylated proteins rebutted the idea about substantial oxidative stress in chronically irradiated plants. We advocate the necessity to consider plausibly increased pathogen sensitivity while developing policies for the management of radionuclide-contaminated areas.
2025-05-07 | PXD060551 | Pride
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 | GSE238133 | 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: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:The Lemnaceae (duckweeds) are the world’s smallest but fastest growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production, and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis of Lemna genomes that uncover candidate genes responsible for the unique metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly among Lemna, and we have found mutations in highly-conserved meiotic crossover genes that could support polyploid meiosis. Further, mapping centromeres by chromatin immunoprecipitation suggests their epigenetic origin despite divergence of underlying tandem repeats and centromeric retrotransposons. Syntenic comparisons with Wolffia and Spirodela reveal that diversification of these genera coincided with the “Azolla event” in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2 levels to those of the current ice age. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by recent engineering of high-oil Lemna that outperforms oil seed crops.
2025-02-04 | GSE288765 | GEO
Project description:Fungal samples of three different plants from wetlands Metagenome
| PRJNA881951 | ENA