Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant <i>Clematis florida</i> Thunb. var. <i>plena</i> D. Don

HE Shulan; KE Lanlan; CHEN Guanshui

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HE S L, KE L L, CHEN G S. Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−10

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HE S L, KE L L, CHEN G S. Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don [J]. Fujian Journal of Agricultural Sciences，2024，39（9）：1−10

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Full-length Transcriptome Sequencing Analysis for She medicine ‘Shi Er Shi Chen’ of original plant Clematis florida Thunb. var. plena D. Don

1.
School of Pharmacy, Fujian Health College, Fuzhou, Fujian　350101, China
2.
School of Basic Medical Science , Fujian Medical University Fuzhou, Fujian　350108, China
3.
College of Life Science, Fuian Agriculture and Forestry University, Fuzhou, Fujian　350002, China

Received Date: 2024-08-02
Accepted Date: 2024-10-16
Rev Recd Date: 2024-09-12

Available Online: 2024-11-11

Abstract

Abstract

Objective Clematis florida Thunb. var. plena D. Don is used in She medicine "Shi Er Shi Chen". Its roots, rich in active compounds, are used medicinally. This study aims to understand the gene annotation, secondary metabolite pathways, and gene functions of Clematis florida Thunb. var. plena D. Don. The goal is to enrich its transcriptome information and lay the foundation for further screening and identification of key genes involved in the metabolic pathways of its medicinal compounds, as well as supporting molecular breeding efforts. Method In this study, the PacBio single-molecule real-time (SMRT) SMRT sequencing was used to generate the full-length transcriptome data of the roots of Clematis florida Thunb. var. plena D. Don. Functional annotation, gene structure analysis, and mining of the terpenoid biosynthetic pathway were conductedusing bioinfromatics tools on the obtained transcript data. Result A total of 62.21 G polymerase read bases were generated, finally 20540 non-redundant high-quality transcript sequences were successfully identified. Gene function annotation was carried out against seven major databases, including NR, NT, Pfam, COG/KOG, SwissProt, GO andKEGG. A total of 19,909 transcripts were successfully annotated in at least one public database, and 8,888 transcripts were annotated in five common databases (NR, NT, COG/KOG, KEGG, GO). GO annotation results showed that 14,911 transcripts were enriched in 53 terms, including biological processes, cellular components, and molecular functions. A total of 19,701 transcripts wrere annotated to KEGGdatabase and classified to 6 major pathways and 44 sub-pathways, with the largest number of transcripts enriched in metabolic pathways. COG/KOG annotation identified 13,204 transcripts, with general function prediction being the most predominant.. A total of 978 transcription factors, 224 lncRNAs, and 7,167 SSRs were predicted. A total of 48 transcripts (16 key candidate genes) involved in terpenoid backbone biosynthesis were identified. Conclusion This study successfully performed full-length transcriptome sequencing of the roots of Clematis florida Thunb. var. plena D. Don, obtaining comprehensive gene function information for this species. It fills the gap in the gene information of Clematis florida Thunb. var. plena D. Don and provides a reference for further studies on its regulatory network, biological characteristics, related metabolic pathways, signaling pathways, and molecular mechanisms.
- Clematis florida,
- full-length transcriptome,
- transcription,
- LncRNA

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References(19)

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