Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea).
Nitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, bioma...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0232011 |
| _version_ | 1818933675207688192 |
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| author | Vijay Joshi Madhumita Joshi Arianne Penalosa |
| author_facet | Vijay Joshi Madhumita Joshi Arianne Penalosa |
| author_sort | Vijay Joshi |
| collection | DOAJ |
| description | Nitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, biomass accumulation, amino acid profiles, and partitioning of N across tissues. RNA-seq analysis revealed that N stress caused most transcriptomic changes in roots, identifying 1,346 DEGs. High-affinity nitrate transporters (NRT2.1, NRT2.5) and glutamine amidotransferase (GAT1) genes were strongly induced in roots in response to N deplete and replete conditions, respectively. GO and KEGG analyses revealed that the functions associated with metabolic pathways and nutrient reservoir activity were enriched due to N stress. Whereas KEGG pathway enrichment analysis indicated the upregulation of DEGs associated with DNA replication, pyrimidine, and purine metabolism in the presence of high N in leaf tissue. A subset of transcription factors comprising bHLH, MYB, WRKY, and AP2/ERF family members was over-represented in both tissues in response to N perturbation. Interesting DEGs associated with N uptake, amino acid metabolism, hormonal pathway, carbon metabolism, along with transcription factors, were highlighted. The results provide valuable information about the underlying molecular processes in response to N stress in spinach and; could serve as a resource for functional analysis of candidate genes/pathways and enhancement of nitrogen use efficiency. |
| first_indexed | 2024-12-20T04:52:09Z |
| format | Article |
| id | doaj.art-86665dd7c14e493dab42ae2e813b5685 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T04:52:09Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-86665dd7c14e493dab42ae2e813b56852022-12-21T19:52:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-01155e023201110.1371/journal.pone.0232011Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea).Vijay JoshiMadhumita JoshiArianne PenalosaNitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, biomass accumulation, amino acid profiles, and partitioning of N across tissues. RNA-seq analysis revealed that N stress caused most transcriptomic changes in roots, identifying 1,346 DEGs. High-affinity nitrate transporters (NRT2.1, NRT2.5) and glutamine amidotransferase (GAT1) genes were strongly induced in roots in response to N deplete and replete conditions, respectively. GO and KEGG analyses revealed that the functions associated with metabolic pathways and nutrient reservoir activity were enriched due to N stress. Whereas KEGG pathway enrichment analysis indicated the upregulation of DEGs associated with DNA replication, pyrimidine, and purine metabolism in the presence of high N in leaf tissue. A subset of transcription factors comprising bHLH, MYB, WRKY, and AP2/ERF family members was over-represented in both tissues in response to N perturbation. Interesting DEGs associated with N uptake, amino acid metabolism, hormonal pathway, carbon metabolism, along with transcription factors, were highlighted. The results provide valuable information about the underlying molecular processes in response to N stress in spinach and; could serve as a resource for functional analysis of candidate genes/pathways and enhancement of nitrogen use efficiency.https://doi.org/10.1371/journal.pone.0232011 |
| spellingShingle | Vijay Joshi Madhumita Joshi Arianne Penalosa Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). PLoS ONE |
| title | Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). |
| title_full | Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). |
| title_fullStr | Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). |
| title_full_unstemmed | Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). |
| title_short | Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). |
| title_sort | comparative analysis of tissue specific transcriptomic responses to nitrogen stress in spinach spinacia oleracea |
| url | https://doi.org/10.1371/journal.pone.0232011 |
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