De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance
Background and objective: Flavonoids are important botanical metabolites, which not only protect plants from harm but also exhibit a variety of biological activities. The aim of this study was to examine the transcriptomic profiles of Abrus cantoniensis (AC) and determine the differentially expresse...
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KeAi Communications Co., Ltd.
2021-12-01
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| Series: | Journal of Holistic Integrative Pharmacy |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2707368823000730 |
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| author | Weibin HUANG Yu QIU Zhixia CHEN Cuimin HE Xianmei XUE Xujiang YUAN |
| author_facet | Weibin HUANG Yu QIU Zhixia CHEN Cuimin HE Xianmei XUE Xujiang YUAN |
| author_sort | Weibin HUANG |
| collection | DOAJ |
| description | Background and objective: Flavonoids are important botanical metabolites, which not only protect plants from harm but also exhibit a variety of biological activities. The aim of this study was to examine the transcriptomic profiles of Abrus cantoniensis (AC) and determine the differentially expressed genes (DEGs) of flavonoids in the roots (AC-R), stems (AC-S), mature leaves (AC-ML), and tender leaves (AC-TL) of this medicinal plant. Methods: Illumina sequencing technology was applied to sequence the transcriptome of AC. Bioinformatics tools were used to perform the de novo assembly, genes annotation, cluster analysis. Results: More than 99.70% clean reads with 57 325 assembled unigenes were obtained. A total of 36 947 unigenes (64.45%) were successfully annotated in the Nr, SwissProt, KOG, and KEGG databases; 8 269 unigenes were assigned to 132 pathways in the KEGG database. Differential gene analysis revealed meaningful differences in the number of up- and down-regulated genes among the different parts of AC, except between AC-R and AC-S. Cluster analysis of the expression patterns of the DEGs revealed different expression trends for 20 profiles among which 9 were remarkably enriched. The most obvious difference in gene expression among AC-R, AC-S, AC-ML, and AC-TL with respect to the biosynthesis of phenylpropanoids was detected upstream in the flavonoid metabolic pathway. Conclusion: This is the first study to provide information about the transcriptome profiles of AC and the DEGs of the flavonoid pathway in this plant. |
| format | Article |
| id | doaj-art-e9734ae40cbb4ad9bd7b6b94df2022a0 |
| institution | Kabale University |
| issn | 2707-3688 |
| language | English |
| publishDate | 2021-12-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Holistic Integrative Pharmacy |
| spelling | doaj-art-e9734ae40cbb4ad9bd7b6b94df2022a02024-11-12T05:21:38ZengKeAi Communications Co., Ltd.Journal of Holistic Integrative Pharmacy2707-36882021-12-0124301319De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis HanceWeibin HUANG0Yu QIU1Zhixia CHEN2Cuimin HE3Xianmei XUE4Xujiang YUAN5Center for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaCenter for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaNew Zealand Health Manufacturing, Auckland 2022, New ZealandCenter for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaCenter for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaCenter for Drug Research and Development/Class III Laboratory of Modern Chinese Medicine Preparation, State Administration of Traditional Chinese Medicine of the P.R.C/ Key Laboratory of modern Chinese medicine of Education Department of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China; Corresponding authorBackground and objective: Flavonoids are important botanical metabolites, which not only protect plants from harm but also exhibit a variety of biological activities. The aim of this study was to examine the transcriptomic profiles of Abrus cantoniensis (AC) and determine the differentially expressed genes (DEGs) of flavonoids in the roots (AC-R), stems (AC-S), mature leaves (AC-ML), and tender leaves (AC-TL) of this medicinal plant. Methods: Illumina sequencing technology was applied to sequence the transcriptome of AC. Bioinformatics tools were used to perform the de novo assembly, genes annotation, cluster analysis. Results: More than 99.70% clean reads with 57 325 assembled unigenes were obtained. A total of 36 947 unigenes (64.45%) were successfully annotated in the Nr, SwissProt, KOG, and KEGG databases; 8 269 unigenes were assigned to 132 pathways in the KEGG database. Differential gene analysis revealed meaningful differences in the number of up- and down-regulated genes among the different parts of AC, except between AC-R and AC-S. Cluster analysis of the expression patterns of the DEGs revealed different expression trends for 20 profiles among which 9 were remarkably enriched. The most obvious difference in gene expression among AC-R, AC-S, AC-ML, and AC-TL with respect to the biosynthesis of phenylpropanoids was detected upstream in the flavonoid metabolic pathway. Conclusion: This is the first study to provide information about the transcriptome profiles of AC and the DEGs of the flavonoid pathway in this plant.http://www.sciencedirect.com/science/article/pii/S2707368823000730Abrus cantoniensis HanceEnzymesFlavonoidsmRNATranscriptome |
| spellingShingle | Weibin HUANG Yu QIU Zhixia CHEN Cuimin HE Xianmei XUE Xujiang YUAN De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance Journal of Holistic Integrative Pharmacy Abrus cantoniensis Hance Enzymes Flavonoids mRNA Transcriptome |
| title | De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance |
| title_full | De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance |
| title_fullStr | De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance |
| title_full_unstemmed | De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance |
| title_short | De novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in Abrus cantoniensis Hance |
| title_sort | de novo transcriptome sequencing and analysis of genes related to flavonoid metabolism in abrus cantoniensis hance |
| topic | Abrus cantoniensis Hance Enzymes Flavonoids mRNA Transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S2707368823000730 |
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