Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum
M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we con...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1215044/full |
| _version_ | 1827891636428865536 |
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| author | Hui Li Hui Li Wei Wang Rui Liu Botong Tong Botong Tong Xinren Dai Yan Lu Yixun Yu Seping Dai Lin Ruan |
| author_facet | Hui Li Hui Li Wei Wang Rui Liu Botong Tong Botong Tong Xinren Dai Yan Lu Yixun Yu Seping Dai Lin Ruan |
| author_sort | Hui Li |
| collection | DOAJ |
| description | M. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development. |
| first_indexed | 2024-03-12T21:28:37Z |
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| id | doaj.art-749fa6116d8847c9a936e07c7fc5a502 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-12T21:28:37Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-749fa6116d8847c9a936e07c7fc5a5022023-07-28T00:37:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-07-011410.3389/fpls.2023.12150441215044Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidumHui Li0Hui Li1Wei Wang2Rui Liu3Botong Tong4Botong Tong5Xinren Dai6Yan Lu7Yixun Yu8Seping Dai9Lin Ruan10Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, ChinaDepartment of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, ChinaState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, ChinaJiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Nanjing, Jiangsu, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, ChinaDepartment of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, ChinaDepartment of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, ChinaM. candidum, an evergreen shrubby flower known for its superior adaptation ability in South China, has gained increased attention in garden applications. However, scant attention has been paid to its flower development and color formation process at the non-coding RNA level. To fill this gap, we conducted a comprehensive analysis based on long non-coding RNA sequencing (lncRNA-seq), RNA-seq, small RNA sequencing (sRNA-seq), and widely targeted metabolome detection of three different flower developmental stages of M. candidum. After differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs), differentially expressed microRNAs (DEmiRNAs), and differentially synthesized metabolites (DSmets) analyses between the different flower developmental stages, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to identify some key genes and metabolites in flavonoid, flavone, anthocyanin, carotenoid, and alkaloid-related GO terms and biosynthetic pathways. Three direct-acting models, including antisense-acting, cis-acting, and trans-acting between lncRNAs and mRNAs, were detected to illustrate the direct function of lncRNAs on target genes during flower development and color formation. Based on the competitive endogenous RNA (ceRNA) regulatory theory, we constructed a lncRNA-mediated regulatory network composed of DElncRNAs, DEmiRNAs, DEmRNAs, and DSmets to elucidate the indirect role of lncRNAs in the flower development and color formation of M. candidum. By utilizing correlation analyses between DERNAs and DSmets within the ceRNA regulatory network, alongside verification trials of the ceRNA regulatory mechanism, the study successfully illustrated the significance of lncRNAs in flower development and color formation process. This research provides a foundation for improving and regulating flower color at the lncRNA level in M. candidum, and sheds light on the potential applications of non-coding RNA in studies of flower development. https://www.frontiersin.org/articles/10.3389/fpls.2023.1215044/fulllncRNAceRNA regulatory mechanismflower developmentflower color formationmetabolitesMelastoma candidum |
| spellingShingle | Hui Li Hui Li Wei Wang Rui Liu Botong Tong Botong Tong Xinren Dai Yan Lu Yixun Yu Seping Dai Lin Ruan Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum Frontiers in Plant Science lncRNA ceRNA regulatory mechanism flower development flower color formation metabolites Melastoma candidum |
| title | Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum |
| title_full | Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum |
| title_fullStr | Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum |
| title_full_unstemmed | Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum |
| title_short | Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum |
| title_sort | long non coding rna mediated competing endogenous rna regulatory network during flower development and color formation in melastoma candidum |
| topic | lncRNA ceRNA regulatory mechanism flower development flower color formation metabolites Melastoma candidum |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1215044/full |
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