Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation
Abstract Bachground Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candidate genes involved in flavonoid biosynthesis and accumulation, we an...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5354-x |
| _version_ | 1818270549634187264 |
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| author | Wenxian Liang Lin Ni Rebeca Carballar-Lejarazú Xiaoxing Zou Weihong Sun Lingjiao Wu Xueyuan Yuan Yanling Mao Wei Huang Shuangquan Zou |
| author_facet | Wenxian Liang Lin Ni Rebeca Carballar-Lejarazú Xiaoxing Zou Weihong Sun Lingjiao Wu Xueyuan Yuan Yanling Mao Wei Huang Shuangquan Zou |
| author_sort | Wenxian Liang |
| collection | DOAJ |
| description | Abstract Bachground Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candidate genes involved in flavonoid biosynthesis and accumulation, we analyzed transcriptome data from three E. konishii tissues (leaf, branch and capsule) using Illumina Hiseq 2000 platform. Results A total of 91.7, 100.3 and 100.1million clean reads were acquired for the leaf, branch and capsule, respectively; and 85,342 unigenes with a mean length of 893.60 bp and N50 length of 1307 nt were assembled using Trinity program. BLASTx analysis allowed to annotate 40,218 unigenes using public protein databases, including NR, KOG/COG/eggNOG, Swiss-Prot, KEGG and GO. A total of 14,291 (16.75%) unigenes were assigned to 128 KEGG pathways, and 900 unigenes were annotated into 22 KEGG secondary metabolites, including flavonoid biosynthesis. The structure enzymes involved in flavonoid biosynthesis, such as phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate CoA ligase, shikimate O-hydroxycinnamoyltransferase, coumaroylquinate 3′-monooxygenase, caffeoyl-CoA O-methyltransferase, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase, flavonolsynthese, dihydroflavonol 4-reductase, anthocyanidinreductase, leucoanthocyanidin dioxygenase, leucoanthocyanidin reductase, were identified in the transcriptome data, 40 UDP-glycosyltransferase (UGT), 122 Cytochrome P450 (CYP) and 25 O-methyltransferase (OMT) unigenes were also found. A total of 295 unigenes involved in flavonoid transport and 220 transcription factors (97 MYB, 84 bHLH and 39 WD40) were identified. Furthermore, their expression patterns among different tissues were analyzed by DESeq, the differentially expressed genes may play important roles in tissues-specific synthesis, accumulation and modification of flavonoids. Conclusion We present here the de novo transcriptome analysis of E. konishii and the identification of candidate genes involved in biosynthesis and accumulation of flavonoid. In general, these results are an important resource for further research on gene expression, genomic and functional genomics in E. konishii and other related species. |
| first_indexed | 2024-12-12T21:12:03Z |
| format | Article |
| id | doaj.art-43dc172952b3417d95542006ec378036 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T21:12:03Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-43dc172952b3417d95542006ec3780362022-12-22T00:11:51ZengBMCBMC Genomics1471-21642019-01-0120111410.1186/s12864-018-5354-xComparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulationWenxian Liang0Lin Ni1Rebeca Carballar-Lejarazú2Xiaoxing Zou3Weihong Sun4Lingjiao Wu5Xueyuan Yuan6Yanling Mao7Wei Huang8Shuangquan Zou9College of Forestry, Fujian Agriculture and Forestry UniversityFujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry UniversityDepartment of Microbiology & Molecular Genetics, University of CaliforniaCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityFujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry UniversityFujian Colleges and Universities Engineering Research Institute of Conservation & Utilization of Natural Bioresources, Fujian Agriculture and Forestry UniversityCollege of Forestry, Fujian Agriculture and Forestry UniversityAbstract Bachground Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candidate genes involved in flavonoid biosynthesis and accumulation, we analyzed transcriptome data from three E. konishii tissues (leaf, branch and capsule) using Illumina Hiseq 2000 platform. Results A total of 91.7, 100.3 and 100.1million clean reads were acquired for the leaf, branch and capsule, respectively; and 85,342 unigenes with a mean length of 893.60 bp and N50 length of 1307 nt were assembled using Trinity program. BLASTx analysis allowed to annotate 40,218 unigenes using public protein databases, including NR, KOG/COG/eggNOG, Swiss-Prot, KEGG and GO. A total of 14,291 (16.75%) unigenes were assigned to 128 KEGG pathways, and 900 unigenes were annotated into 22 KEGG secondary metabolites, including flavonoid biosynthesis. The structure enzymes involved in flavonoid biosynthesis, such as phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate CoA ligase, shikimate O-hydroxycinnamoyltransferase, coumaroylquinate 3′-monooxygenase, caffeoyl-CoA O-methyltransferase, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3′-hydroxylase, flavonoid 3′,5′-hydroxylase, flavonolsynthese, dihydroflavonol 4-reductase, anthocyanidinreductase, leucoanthocyanidin dioxygenase, leucoanthocyanidin reductase, were identified in the transcriptome data, 40 UDP-glycosyltransferase (UGT), 122 Cytochrome P450 (CYP) and 25 O-methyltransferase (OMT) unigenes were also found. A total of 295 unigenes involved in flavonoid transport and 220 transcription factors (97 MYB, 84 bHLH and 39 WD40) were identified. Furthermore, their expression patterns among different tissues were analyzed by DESeq, the differentially expressed genes may play important roles in tissues-specific synthesis, accumulation and modification of flavonoids. Conclusion We present here the de novo transcriptome analysis of E. konishii and the identification of candidate genes involved in biosynthesis and accumulation of flavonoid. In general, these results are an important resource for further research on gene expression, genomic and functional genomics in E. konishii and other related species.http://link.springer.com/article/10.1186/s12864-018-5354-xEuscaphis konishii HayataTranscriptomeGene expressionFlavonoidBiosynthesisTransport |
| spellingShingle | Wenxian Liang Lin Ni Rebeca Carballar-Lejarazú Xiaoxing Zou Weihong Sun Lingjiao Wu Xueyuan Yuan Yanling Mao Wei Huang Shuangquan Zou Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation BMC Genomics Euscaphis konishii Hayata Transcriptome Gene expression Flavonoid Biosynthesis Transport |
| title | Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| title_full | Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| title_fullStr | Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| title_full_unstemmed | Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| title_short | Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| title_sort | comparative transcriptome among euscaphis konishii hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation |
| topic | Euscaphis konishii Hayata Transcriptome Gene expression Flavonoid Biosynthesis Transport |
| url | http://link.springer.com/article/10.1186/s12864-018-5354-x |
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