Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl
Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of Coll.et Hemsl. were studied to expl...
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| Veröffentlicht in: | Genes 2024-07, Vol.15 (7), p.828 |
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| description | Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of
Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in
Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (
,
,
,
,
,
,
,
,
,
,
,
, and
) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in
Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species. |
| doi_str_mv | 10.3390/genes15070828 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_3085115106</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A803772188</galeid><sourcerecordid>A803772188</sourcerecordid><originalsourceid>FETCH-LOGICAL-c313t-4b4c329b1dcd32efaee74b080504f39729bd354ff2c2ab690e41670ae093a5ae3</originalsourceid><addsrcrecordid>eNptkk1vEzEQhlcVqK1Kj1yRJS5cNow_9usYhYZWKqKqynlle2eDi9cOthcpv4U_i9O0qEV4Dh69ft7RaDxF8ZbCgvMOPm7QYaQVNNCy9qg4ZdDwUghWvXqWnxTnMd5DPgIYQHVcnGRvzWpoTovfKz8p43AgXzBJ5a2fjI5EuoHcBemiDmabDtrSSbuLJhI_kvQdyScTUzBqTsa7vba28pd33gyRGPdArI0Kfo7k1vt0KCm3YZ9n-sbb3cY7meaJ_DBuY6TL2cpbu8BELnGK9k3xepQ24vnjfVZ8W1_crS7L66-fr1bL61JzylMplNCcdYoOeuAMR4nYCAUtVCBG3jX5aeCVGEemmVR1Byho3YBE6LisJPKz4sOhbm7u54wx9ZOJGq2VDnP7PYe2orSiUGf0_T_ovZ9DHswDJTrgTfeM2kiLvXGjT0HqfdF-2WakYbRtM7X4D5VjwDxv73A0WX9hKA8GHXyMAcd-G8wkw66n0O_3oX-xD5l_99jsrCYc_tJPv8__AG1TsZA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3084903796</pqid></control><display><type>article</type><title>Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl</title><source>MEDLINE</source><source>PubMed Central Open Access</source><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Mo, Xinchun ; Wang, Ling ; Yu, Chenghua ; Kou, Can</creator><creatorcontrib>Mo, Xinchun ; Wang, Ling ; Yu, Chenghua ; Kou, Can</creatorcontrib><description>Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of
Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in
Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (
,
,
,
,
,
,
,
,
,
,
,
, and
) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in
Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes15070828</identifier><identifier>PMID: 39062607</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amino acids ; Analysis ; Biosynthesis ; Biosynthetic Pathways - genetics ; Enzymes ; Flavonoids ; Flavonoids - biosynthesis ; Flavonoids - genetics ; Flavonoids - metabolism ; Flavonols ; Flow velocity ; Gene Expression Profiling - methods ; Gene Expression Regulation, Plant ; Herbal medicine ; Information processing ; Isoflavones ; Mass spectrometry ; Medicinal plants ; Metabolites ; Metabolomics ; Metabolomics - methods ; Phenolic acids ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant Roots - genetics ; Plant Roots - metabolism ; Polygonatum ; Polygonatum - genetics ; Polygonatum - metabolism ; Rhizomes ; Roots ; Saponins ; Scientific imaging ; Secondary metabolites ; Solvents ; Steroid hormones ; Transcriptome ; Transcriptomes ; Transcriptomics</subject><ispartof>Genes, 2024-07, Vol.15 (7), p.828</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c313t-4b4c329b1dcd32efaee74b080504f39729bd354ff2c2ab690e41670ae093a5ae3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39062607$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mo, Xinchun</creatorcontrib><creatorcontrib>Wang, Ling</creatorcontrib><creatorcontrib>Yu, Chenghua</creatorcontrib><creatorcontrib>Kou, Can</creatorcontrib><title>Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of
Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in
Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (
,
,
,
,
,
,
,
,
,
,
,
, and
) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in
Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Biosynthesis</subject><subject>Biosynthetic Pathways - genetics</subject><subject>Enzymes</subject><subject>Flavonoids</subject><subject>Flavonoids - biosynthesis</subject><subject>Flavonoids - genetics</subject><subject>Flavonoids - metabolism</subject><subject>Flavonols</subject><subject>Flow velocity</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene Expression Regulation, Plant</subject><subject>Herbal medicine</subject><subject>Information processing</subject><subject>Isoflavones</subject><subject>Mass spectrometry</subject><subject>Medicinal plants</subject><subject>Metabolites</subject><subject>Metabolomics</subject><subject>Metabolomics - methods</subject><subject>Phenolic acids</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant Roots - genetics</subject><subject>Plant Roots - metabolism</subject><subject>Polygonatum</subject><subject>Polygonatum - genetics</subject><subject>Polygonatum - metabolism</subject><subject>Rhizomes</subject><subject>Roots</subject><subject>Saponins</subject><subject>Scientific imaging</subject><subject>Secondary metabolites</subject><subject>Solvents</subject><subject>Steroid hormones</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><subject>Transcriptomics</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptkk1vEzEQhlcVqK1Kj1yRJS5cNow_9usYhYZWKqKqynlle2eDi9cOthcpv4U_i9O0qEV4Dh69ft7RaDxF8ZbCgvMOPm7QYaQVNNCy9qg4ZdDwUghWvXqWnxTnMd5DPgIYQHVcnGRvzWpoTovfKz8p43AgXzBJ5a2fjI5EuoHcBemiDmabDtrSSbuLJhI_kvQdyScTUzBqTsa7vba28pd33gyRGPdArI0Kfo7k1vt0KCm3YZ9n-sbb3cY7meaJ_DBuY6TL2cpbu8BELnGK9k3xepQ24vnjfVZ8W1_crS7L66-fr1bL61JzylMplNCcdYoOeuAMR4nYCAUtVCBG3jX5aeCVGEemmVR1Byho3YBE6LisJPKz4sOhbm7u54wx9ZOJGq2VDnP7PYe2orSiUGf0_T_ovZ9DHswDJTrgTfeM2kiLvXGjT0HqfdF-2WakYbRtM7X4D5VjwDxv73A0WX9hKA8GHXyMAcd-G8wkw66n0O_3oX-xD5l_99jsrCYc_tJPv8__AG1TsZA</recordid><startdate>20240701</startdate><enddate>20240701</enddate><creator>Mo, Xinchun</creator><creator>Wang, Ling</creator><creator>Yu, Chenghua</creator><creator>Kou, Can</creator><general>MDPI AG</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20240701</creationdate><title>Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl</title><author>Mo, Xinchun ; Wang, Ling ; Yu, Chenghua ; Kou, Can</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c313t-4b4c329b1dcd32efaee74b080504f39729bd354ff2c2ab690e41670ae093a5ae3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Biosynthesis</topic><topic>Biosynthetic Pathways - genetics</topic><topic>Enzymes</topic><topic>Flavonoids</topic><topic>Flavonoids - biosynthesis</topic><topic>Flavonoids - genetics</topic><topic>Flavonoids - metabolism</topic><topic>Flavonols</topic><topic>Flow velocity</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene Expression Regulation, Plant</topic><topic>Herbal medicine</topic><topic>Information processing</topic><topic>Isoflavones</topic><topic>Mass spectrometry</topic><topic>Medicinal plants</topic><topic>Metabolites</topic><topic>Metabolomics</topic><topic>Metabolomics - methods</topic><topic>Phenolic acids</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plant Roots - genetics</topic><topic>Plant Roots - metabolism</topic><topic>Polygonatum</topic><topic>Polygonatum - genetics</topic><topic>Polygonatum - metabolism</topic><topic>Rhizomes</topic><topic>Roots</topic><topic>Saponins</topic><topic>Scientific imaging</topic><topic>Secondary metabolites</topic><topic>Solvents</topic><topic>Steroid hormones</topic><topic>Transcriptome</topic><topic>Transcriptomes</topic><topic>Transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mo, Xinchun</creatorcontrib><creatorcontrib>Wang, Ling</creatorcontrib><creatorcontrib>Yu, Chenghua</creatorcontrib><creatorcontrib>Kou, Can</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mo, Xinchun</au><au>Wang, Ling</au><au>Yu, Chenghua</au><au>Kou, Can</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2024-07-01</date><risdate>2024</risdate><volume>15</volume><issue>7</issue><spage>828</spage><pages>828-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of
Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in
Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (
,
,
,
,
,
,
,
,
,
,
,
, and
) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in
Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39062607</pmid><doi>10.3390/genes15070828</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Amino acids Analysis Biosynthesis Biosynthetic Pathways - genetics Enzymes Flavonoids Flavonoids - biosynthesis Flavonoids - genetics Flavonoids - metabolism Flavonols Flow velocity Gene Expression Profiling - methods Gene Expression Regulation, Plant Herbal medicine Information processing Isoflavones Mass spectrometry Medicinal plants Metabolites Metabolomics Metabolomics - methods Phenolic acids Plant Proteins - genetics Plant Proteins - metabolism Plant Roots - genetics Plant Roots - metabolism Polygonatum Polygonatum - genetics Polygonatum - metabolism Rhizomes Roots Saponins Scientific imaging Secondary metabolites Solvents Steroid hormones Transcriptome Transcriptomes Transcriptomics |
| title | Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl |
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