Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues
Abstract Background Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehen...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-019-2138-7 |
| _version_ | 1819076474150322176 |
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| author | Yingdan Yuan Jinchi Zhang Justin Kallman Xin Liu Miaojing Meng Jie Lin |
| author_facet | Yingdan Yuan Jinchi Zhang Justin Kallman Xin Liu Miaojing Meng Jie Lin |
| author_sort | Yingdan Yuan |
| collection | DOAJ |
| description | Abstract Background Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme. Results In our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. Conclusions We determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb. |
| first_indexed | 2024-12-21T18:41:52Z |
| format | Article |
| id | doaj.art-32f06fb029c54dcab0aab18ce93c04f6 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T18:41:52Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-32f06fb029c54dcab0aab18ce93c04f62022-12-21T18:54:00ZengBMCBMC Plant Biology1471-22292019-11-0119111910.1186/s12870-019-2138-7Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissuesYingdan Yuan0Jinchi Zhang1Justin Kallman2Xin Liu3Miaojing Meng4Jie Lin5Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityUniversity of MiamiCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry UniversityAbstract Background Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme. Results In our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. Conclusions We determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.http://link.springer.com/article/10.1186/s12870-019-2138-7Dendrobium moniliformeTranscriptomePolysaccharides synthesisGlycosyltransferase |
| spellingShingle | Yingdan Yuan Jinchi Zhang Justin Kallman Xin Liu Miaojing Meng Jie Lin Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues BMC Plant Biology Dendrobium moniliforme Transcriptome Polysaccharides synthesis Glycosyltransferase |
| title | Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues |
| title_full | Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues |
| title_fullStr | Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues |
| title_full_unstemmed | Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues |
| title_short | Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues |
| title_sort | polysaccharide biosynthetic pathway profiling and putative gene mining of dendrobium moniliforme using rna seq in different tissues |
| topic | Dendrobium moniliforme Transcriptome Polysaccharides synthesis Glycosyltransferase |
| url | http://link.springer.com/article/10.1186/s12870-019-2138-7 |
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