Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1194111 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31606300_1.fastq.gz | Fastqsanger.gz | |||
| SRR31606300_2.fastq.gz | Fastqsanger.gz | |||
| SRR31606301_1.fastq.gz | Fastqsanger.gz | |||
| SRR31606301_2.fastq.gz | Fastqsanger.gz | |||
| SRR31606302_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite the broad use of single-cell and single-nucleus RNA sequencing in plant research, accurate cluster annotation in less studied plant species remains a major challenge due to the lack of validated marker genes. Here, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.
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Project description:Despite the broad use of single-cell and single-nucleus RNA sequencing in plant research, accurate cluster annotation in less studied plant species remains a major challenge due to the lack of validated marker genes. Here, using soil-grown wheat roots as a model, we generated a single-cell RNA-sequencing (scRNA-seq) atlas and annotated cluster identities in an unbiased way by transferring existing annotations from publicly available datasets in wheat, rice, maize and Arabidopsis. These cross-species orthology-based predictions were next validated using untargeted spatial transcriptomics. This information refined existing cluster annotations for different datasets across key plant model species. We then used the validated clusters to generate cell type-specific gene regulatory networks for root tissues of wheat and two other monocot crop species. By integrating all available data, including homeolog expression in wheat, we predicted reliable tissue-specific markers which are conserved across different species. In summary, we provided an annotated and validated single cell transcriptomic resource for soil-grown wheat root apical meristems and revealed conserved cell type-specific regulators and markers across species. These data expand upon previous root single cell atlas resources in crops, and will facilitate cell type annotation in non-model plant species in the future.
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Project description:Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties, plant and microbial communities, in particular microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38-137% in response to either clipping or the combined treatment, which could weaken the long-term soil carbon stability and trigger a positive feedback to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization and denitrification by 32-39%. The potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium caused by clipping alone, and contribute to unchanged plant biomass. Moreover, clipping tended to interact antagonistically with warming, especially on nitrogen cycling genes, demonstrating that single factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties, as well as the abundance and structure of soil microbial functional genes. The aboveground biomass removal for biofuel production needs to be re-considered as the long-term soil carbon stability may be weakened.
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