Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li
<i>Cinnamomum migao</i> H. W. Li is an evergreen woody plant that is only distributed in southwest China. The volatile oils from the fruits of <i>C. migao</i> have long been used as a special authentic medicinal herb by local ethnic minorities. Due to its low seed germination...
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MDPI AG
2023-10-01
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| Online Access: | https://www.mdpi.com/1999-4907/14/10/2075 |
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| author | Zhigang Ju Qiuling Gong Lin Liang Dejing Kong Tao Zhou Wei Sun Yuxin Pang Yongping Zhang |
| author_facet | Zhigang Ju Qiuling Gong Lin Liang Dejing Kong Tao Zhou Wei Sun Yuxin Pang Yongping Zhang |
| author_sort | Zhigang Ju |
| collection | DOAJ |
| description | <i>Cinnamomum migao</i> H. W. Li is an evergreen woody plant that is only distributed in southwest China. The volatile oils from the fruits of <i>C. migao</i> have long been used as a special authentic medicinal herb by local ethnic minorities. Due to its low seed germination rate, destructive lumbering and low rates of artificial planting, <i>C. migao</i> is facing the danger of extinction. Therefore, it is urgent to exploit and protect this species using molecular biological technology, especially to target the genes involved in the biosynthesis of terpenoids in the volatile oil. However, the genomic data for this plant are not available. In this study, the transcriptome sequencing of <i>C. migao</i> was performed to obtain the key genes involved in terpenoid biosynthesis via a combination of full-length transcriptome and next-generation sequencing (NGS). More than 39.9 Gb of raw data was obtained and 515,929 circular consensus sequences (CCSs) were extracted. After clustering similar 472,858 full-length non-chimeric (FLNC) reads and correction with NGS data, 139,871 consensus isoforms were obtained. Meanwhile, 73,575 non-redundant transcripts were generated by removing redundant transcripts. Then, 70,427 isoforms were successfully annotated using public databases. Moreover, differentially expressed transcripts (DETs) in four different developmental stages of the <i>C. migao</i> fruit were analyzed and 5764 transcripts showed period-specific expression. Finally, 15 transcripts, 6 transcripts, and only 1 transcript were identified as being involved in the biosynthesis of sesquiterpenoids, diterpenoids, and monoterpenoids, respectively. This study provides a basis for future research in the gene mining, genetic breeding, and metabolic engineering of <i>C. migao</i>. |
| first_indexed | 2024-03-10T21:14:21Z |
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| language | English |
| last_indexed | 2024-03-10T21:14:21Z |
| publishDate | 2023-10-01 |
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| series | Forests |
| spelling | doaj.art-105c9c81b08547839548ea2ed733d3e92023-11-19T16:33:22ZengMDPI AGForests1999-49072023-10-011410207510.3390/f14102075Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. LiZhigang Ju0Qiuling Gong1Lin Liang2Dejing Kong3Tao Zhou4Wei Sun5Yuxin Pang6Yongping Zhang7Pharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaPharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaPharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaPharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaPharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaKey Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountain Area of Southwest of China, School of Life Science, Guizhou Normal University, Guiyang 550025, ChinaYunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, ChinaPharmacy College, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China<i>Cinnamomum migao</i> H. W. Li is an evergreen woody plant that is only distributed in southwest China. The volatile oils from the fruits of <i>C. migao</i> have long been used as a special authentic medicinal herb by local ethnic minorities. Due to its low seed germination rate, destructive lumbering and low rates of artificial planting, <i>C. migao</i> is facing the danger of extinction. Therefore, it is urgent to exploit and protect this species using molecular biological technology, especially to target the genes involved in the biosynthesis of terpenoids in the volatile oil. However, the genomic data for this plant are not available. In this study, the transcriptome sequencing of <i>C. migao</i> was performed to obtain the key genes involved in terpenoid biosynthesis via a combination of full-length transcriptome and next-generation sequencing (NGS). More than 39.9 Gb of raw data was obtained and 515,929 circular consensus sequences (CCSs) were extracted. After clustering similar 472,858 full-length non-chimeric (FLNC) reads and correction with NGS data, 139,871 consensus isoforms were obtained. Meanwhile, 73,575 non-redundant transcripts were generated by removing redundant transcripts. Then, 70,427 isoforms were successfully annotated using public databases. Moreover, differentially expressed transcripts (DETs) in four different developmental stages of the <i>C. migao</i> fruit were analyzed and 5764 transcripts showed period-specific expression. Finally, 15 transcripts, 6 transcripts, and only 1 transcript were identified as being involved in the biosynthesis of sesquiterpenoids, diterpenoids, and monoterpenoids, respectively. This study provides a basis for future research in the gene mining, genetic breeding, and metabolic engineering of <i>C. migao</i>.https://www.mdpi.com/1999-4907/14/10/2075<i>C. migao</i>volatile oilfunctional annotationterpenoid synthase |
| spellingShingle | Zhigang Ju Qiuling Gong Lin Liang Dejing Kong Tao Zhou Wei Sun Yuxin Pang Yongping Zhang Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li Forests <i>C. migao</i> volatile oil functional annotation terpenoid synthase |
| title | Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li |
| title_full | Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li |
| title_fullStr | Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li |
| title_full_unstemmed | Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li |
| title_short | Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in <i>Cinnamomum migao</i> H. W. Li |
| title_sort | full length transcriptome sequencing and identification of genes related to terpenoid biosynthesis in i cinnamomum migao i h w li |
| topic | <i>C. migao</i> volatile oil functional annotation terpenoid synthase |
| url | https://www.mdpi.com/1999-4907/14/10/2075 |
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