Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications
Cyanide (CN<sup>−</sup>) pollution in agricultural systems can affect crop production. However, no data are available to describe the full picture of the responsive metabolic mechanisms of genes with known functions related to exogenous KCN exposure. In this study, we examined the transc...
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MDPI AG
2022-10-01
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| author | Cheng-Zhi Li Yu-Juan Lin Xiao-Zhang Yu |
| author_facet | Cheng-Zhi Li Yu-Juan Lin Xiao-Zhang Yu |
| author_sort | Cheng-Zhi Li |
| collection | DOAJ |
| description | Cyanide (CN<sup>−</sup>) pollution in agricultural systems can affect crop production. However, no data are available to describe the full picture of the responsive metabolic mechanisms of genes with known functions related to exogenous KCN exposure. In this study, we examined the transcriptome in rice seedlings exposed to potassium cyanide (KCN) using an Agilent 4×44K rice microarray to clarify the relationship between the differentially expressed genes (DEGs) and their function classifications. The number of DEGs (up-regulated genes/down-regulated genes) was 322/626 and 640/948 in the shoots and roots of CN<sup>−</sup>-treated rice seedlings, respectively. Functional predication demonstrated that a total of 534 and 837 DEGs in shoots and roots were assigned to 22 COG categories. Four common categories listed on the top five COG classifications were detected in both rice tissues: signal transduction mechanisms, carbohydrate transport and metabolism, post-translational modification, protein turnover and chaperones, and transcription. A comparison of DEGs aligned to the same COG classification demonstrated that the majority of up-regulated/down-regulated DEGs in rice tissues were significantly different, suggesting that responsive and regulatory mechanisms are tissue specific in CN<sup>−</sup>-treated rice seedlings. Additionally, fifteen DEGs were aligned to three different COG categories, implying their possible multiple functions in response to KCN stress. The results presented here provide insights into the novel responsive and regulatory mechanisms of KCN-responsive genes, and will serve as useful resources for further functional dissections of the physiological significance of specific genes activated in the exogenous KCN stress response in rice plants. |
| first_indexed | 2024-03-09T18:56:06Z |
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| id | doaj.art-c46d3c770f324385884f37acdc1adf4a |
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| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T18:56:06Z |
| publishDate | 2022-10-01 |
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| spelling | doaj.art-c46d3c770f324385884f37acdc1adf4a2023-11-24T05:29:32ZengMDPI AGLife2075-17292022-10-011211170110.3390/life12111701Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional ClassificationsCheng-Zhi Li0Yu-Juan Lin1Xiao-Zhang Yu2The Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology, Guilin 541004, ChinaThe Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology, Guilin 541004, ChinaThe Guangxi Key Laboratory of Theory & Technology for Environmental Pollution Control, College of Environmental Science & Engineering, Guilin University of Technology, Guilin 541004, ChinaCyanide (CN<sup>−</sup>) pollution in agricultural systems can affect crop production. However, no data are available to describe the full picture of the responsive metabolic mechanisms of genes with known functions related to exogenous KCN exposure. In this study, we examined the transcriptome in rice seedlings exposed to potassium cyanide (KCN) using an Agilent 4×44K rice microarray to clarify the relationship between the differentially expressed genes (DEGs) and their function classifications. The number of DEGs (up-regulated genes/down-regulated genes) was 322/626 and 640/948 in the shoots and roots of CN<sup>−</sup>-treated rice seedlings, respectively. Functional predication demonstrated that a total of 534 and 837 DEGs in shoots and roots were assigned to 22 COG categories. Four common categories listed on the top five COG classifications were detected in both rice tissues: signal transduction mechanisms, carbohydrate transport and metabolism, post-translational modification, protein turnover and chaperones, and transcription. A comparison of DEGs aligned to the same COG classification demonstrated that the majority of up-regulated/down-regulated DEGs in rice tissues were significantly different, suggesting that responsive and regulatory mechanisms are tissue specific in CN<sup>−</sup>-treated rice seedlings. Additionally, fifteen DEGs were aligned to three different COG categories, implying their possible multiple functions in response to KCN stress. The results presented here provide insights into the novel responsive and regulatory mechanisms of KCN-responsive genes, and will serve as useful resources for further functional dissections of the physiological significance of specific genes activated in the exogenous KCN stress response in rice plants.https://www.mdpi.com/2075-1729/12/11/1701cyanideCOG classificationsdifferentially expressed genesrice |
| spellingShingle | Cheng-Zhi Li Yu-Juan Lin Xiao-Zhang Yu Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications Life cyanide COG classifications differentially expressed genes rice |
| title | Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications |
| title_full | Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications |
| title_fullStr | Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications |
| title_full_unstemmed | Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications |
| title_short | Transcriptome Analysis of Cyanide-Treated Rice Seedlings: Insights into Gene Functional Classifications |
| title_sort | transcriptome analysis of cyanide treated rice seedlings insights into gene functional classifications |
| topic | cyanide COG classifications differentially expressed genes rice |
| url | https://www.mdpi.com/2075-1729/12/11/1701 |
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