Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia
Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/7/1079 |
| _version_ | 1797445750521593856 |
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| author | Keita Tamura Hidemasa Bono |
| author_facet | Keita Tamura Hidemasa Bono |
| author_sort | Keita Tamura |
| collection | DOAJ |
| description | Hypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA sequencing (RNA-Seq) data of Arabidopsis (<i>Arabidopsis thaliana</i>) and rice (<i>Oryza sativa</i>) under hypoxia. We collected 29 (Arabidopsis) and 26 (rice) pairs of RNA-Seq data involving hypoxic (including submergence) and normoxic (control) treatments and extracted the genes that were commonly upregulated or downregulated in the majority of the experiments. The meta-analysis revealed 40 and 19 commonly upregulated and downregulated genes, respectively, in the two species. Several WRKY transcription factors and cinnamate-4-hydroxylase were commonly upregulated, but their involvement in hypoxia remains unclear. Our meta-analysis identified candidate genes for novel molecular mechanisms in plants under hypoxia. |
| first_indexed | 2024-03-09T13:30:20Z |
| format | Article |
| id | doaj.art-94ce0a404edb4970abb59a9038696f95 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T13:30:20Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-94ce0a404edb4970abb59a9038696f952023-11-30T21:18:29ZengMDPI AGLife2075-17292022-07-01127107910.3390/life12071079Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under HypoxiaKeita Tamura0Hidemasa Bono1Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, JapanLaboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, JapanHypoxia is an abiotic stress in plants. Flooding resulting from climate change is a major crop threat that increases the risk of hypoxic stress. The molecular mechanisms underlying hypoxia in plants were elucidated in recent years, but new genes related to this stress remain to be discovered. Thus, we aimed to perform a meta-analysis of the RNA sequencing (RNA-Seq) data of Arabidopsis (<i>Arabidopsis thaliana</i>) and rice (<i>Oryza sativa</i>) under hypoxia. We collected 29 (Arabidopsis) and 26 (rice) pairs of RNA-Seq data involving hypoxic (including submergence) and normoxic (control) treatments and extracted the genes that were commonly upregulated or downregulated in the majority of the experiments. The meta-analysis revealed 40 and 19 commonly upregulated and downregulated genes, respectively, in the two species. Several WRKY transcription factors and cinnamate-4-hydroxylase were commonly upregulated, but their involvement in hypoxia remains unclear. Our meta-analysis identified candidate genes for novel molecular mechanisms in plants under hypoxia.https://www.mdpi.com/2075-1729/12/7/1079meta-analysishypoxiafloodingsubmergencewaterloggingArabidopsis |
| spellingShingle | Keita Tamura Hidemasa Bono Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia Life meta-analysis hypoxia flooding submergence waterlogging Arabidopsis |
| title | Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia |
| title_full | Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia |
| title_fullStr | Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia |
| title_full_unstemmed | Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia |
| title_short | Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia |
| title_sort | meta analysis of rna sequencing data of arabidopsis and rice under hypoxia |
| topic | meta-analysis hypoxia flooding submergence waterlogging Arabidopsis |
| url | https://www.mdpi.com/2075-1729/12/7/1079 |
| work_keys_str_mv | AT keitatamura metaanalysisofrnasequencingdataofarabidopsisandriceunderhypoxia AT hidemasabono metaanalysisofrnasequencingdataofarabidopsisandriceunderhypoxia |