De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism
Abstract Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosyn...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-020-6521-4 |
| _version_ | 1818412692138885120 |
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| author | Wen-Kai Hui Fei-Yan Zhao Jing-Yan Wang Xiao-Yang Chen Jue-Wei Li Yu Zhong Hong-Yun Li Jun-Xing Zheng Liang-Zhen Zhang Qing-Min Que Ai-Min Wu Wei Gong |
| author_facet | Wen-Kai Hui Fei-Yan Zhao Jing-Yan Wang Xiao-Yang Chen Jue-Wei Li Yu Zhong Hong-Yun Li Jun-Xing Zheng Liang-Zhen Zhang Qing-Min Que Ai-Min Wu Wei Gong |
| author_sort | Wen-Kai Hui |
| collection | DOAJ |
| description | Abstract Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum. |
| first_indexed | 2024-12-14T10:51:21Z |
| format | Article |
| id | doaj.art-e23b88d058c84b75a1a141a5772de391 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T10:51:21Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e23b88d058c84b75a1a141a5772de3912022-12-21T23:05:13ZengBMCBMC Genomics1471-21642020-01-0121111510.1186/s12864-020-6521-4De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolismWen-Kai Hui0Fei-Yan Zhao1Jing-Yan Wang2Xiao-Yang Chen3Jue-Wei Li4Yu Zhong5Hong-Yun Li6Jun-Xing Zheng7Liang-Zhen Zhang8Qing-Min Que9Ai-Min Wu10Wei Gong11Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityGuangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityAgricultural Technology Extension Center in Yantan DistrictKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityGuangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural UniversityKey Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural UniversityAbstract Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.https://doi.org/10.1186/s12864-020-6521-4Zanthoxylum armatumDe novo transcriptomeAromatic compoundsFatty acid |
| spellingShingle | Wen-Kai Hui Fei-Yan Zhao Jing-Yan Wang Xiao-Yang Chen Jue-Wei Li Yu Zhong Hong-Yun Li Jun-Xing Zheng Liang-Zhen Zhang Qing-Min Que Ai-Min Wu Wei Gong De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism BMC Genomics Zanthoxylum armatum De novo transcriptome Aromatic compounds Fatty acid |
| title | De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| title_full | De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| title_fullStr | De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| title_full_unstemmed | De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| title_short | De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| title_sort | de novo transcriptome assembly for the five major organs of zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism |
| topic | Zanthoxylum armatum De novo transcriptome Aromatic compounds Fatty acid |
| url | https://doi.org/10.1186/s12864-020-6521-4 |
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