Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination
Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in...
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MDPI AG
2021-05-01
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| Series: | International Journal of Molecular Sciences |
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| author | Yu Wu Lamei Zheng Jie Bing Huimin Liu Genfa Zhang |
| author_facet | Yu Wu Lamei Zheng Jie Bing Huimin Liu Genfa Zhang |
| author_sort | Yu Wu |
| collection | DOAJ |
| description | Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in <i>A</i><i>tENO2</i> mutation (<i>eno2<sup>−</sup></i>) was earlier than that of wild type (WT) in <i>Arabidopsis thaliana</i>. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including <i>ARF</i> family, <i>TIR1</i>, <i>INVC</i>, <i>RR19</i>, <i>TUDOR2</i>, <i>GA3OX2</i>, <i>PXMT1</i>, and <i>TGA1</i>. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the <i>AtENO2</i> regulation for seed germination. |
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| spelling | doaj.art-af80281b260a48c0a6d4ce4d0212dea12023-11-21T19:15:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-05-012210508810.3390/ijms22105088Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed GerminationYu Wu0Lamei Zheng1Jie Bing2Huimin Liu3Genfa Zhang4Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, ChinaBeijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, ChinaBeijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, ChinaBeijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, ChinaBeijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, ChinaSeed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in <i>A</i><i>tENO2</i> mutation (<i>eno2<sup>−</sup></i>) was earlier than that of wild type (WT) in <i>Arabidopsis thaliana</i>. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including <i>ARF</i> family, <i>TIR1</i>, <i>INVC</i>, <i>RR19</i>, <i>TUDOR2</i>, <i>GA3OX2</i>, <i>PXMT1</i>, and <i>TGA1</i>. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the <i>AtENO2</i> regulation for seed germination.https://www.mdpi.com/1422-0067/22/10/5088seed germination<i>AtENO2</i>miRNAsdeep sequencingregulation network |
| spellingShingle | Yu Wu Lamei Zheng Jie Bing Huimin Liu Genfa Zhang Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination International Journal of Molecular Sciences seed germination <i>AtENO2</i> miRNAs deep sequencing regulation network |
| title | Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination |
| title_full | Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination |
| title_fullStr | Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination |
| title_full_unstemmed | Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination |
| title_short | Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of <i>AtENO2</i> Regulating Seed Germination |
| title_sort | deep sequencing of small rna reveals the molecular regulatory network of i ateno2 i regulating seed germination |
| topic | seed germination <i>AtENO2</i> miRNAs deep sequencing regulation network |
| url | https://www.mdpi.com/1422-0067/22/10/5088 |
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