Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i>
<i>Polygonatum odoratum</i> (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root...
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| Format: | Article |
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MDPI AG
2023-02-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/4/943 |
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| author | Yan Wang Kaitai Liu Yunyun Zhou Yong Chen Chenzhong Jin Yihong Hu |
| author_facet | Yan Wang Kaitai Liu Yunyun Zhou Yong Chen Chenzhong Jin Yihong Hu |
| author_sort | Yan Wang |
| collection | DOAJ |
| description | <i>Polygonatum odoratum</i> (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of <i>P. odoratum</i> roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of <i>p</i>-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of <i>P. odoratum</i> under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of <i>P. odoratum</i>. |
| first_indexed | 2024-03-11T08:14:58Z |
| format | Article |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-11T08:14:58Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-855587e10a6f44198e797ac466f27d812023-11-16T22:49:32ZengMDPI AGPlants2223-77472023-02-0112494310.3390/plants12040943Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i>Yan Wang0Kaitai Liu1Yunyun Zhou2Yong Chen3Chenzhong Jin4Yihong Hu5College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, ChinaCollege of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, ChinaCollege of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, ChinaCollege of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, ChinaCollege of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, ChinaCollege of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China<i>Polygonatum odoratum</i> (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of <i>P. odoratum</i> roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of <i>p</i>-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of <i>P. odoratum</i> under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of <i>P. odoratum</i>.https://www.mdpi.com/2223-7747/12/4/943<i>Polygonatum odoratum</i>root rotsoil phenolicsroot exudatesrootmicroRNA |
| spellingShingle | Yan Wang Kaitai Liu Yunyun Zhou Yong Chen Chenzhong Jin Yihong Hu Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> Plants <i>Polygonatum odoratum</i> root rot soil phenolics root exudates root microRNA |
| title | Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> |
| title_full | Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> |
| title_fullStr | Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> |
| title_full_unstemmed | Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> |
| title_short | Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of <i>Polygonatum odoratum</i> |
| title_sort | integrated analysis of microrna and rna seq reveals phenolic acid secretion metabolism in continuous cropping of i polygonatum odoratum i |
| topic | <i>Polygonatum odoratum</i> root rot soil phenolics root exudates root microRNA |
| url | https://www.mdpi.com/2223-7747/12/4/943 |
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