De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis
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Cornus officinalis Sieb. et Zucc. is a small tree that is recognized with notable medicinal, economic, and ecological values. It has been used as traditional Chinese medicine (TCM) for thousands of years in China. Modern pharmacological research has revealed that cornel iridoid glycosides (CIGs, e.g., loganin and morroniside) in dried pericarp of C. officinalis have significant medicinal activities for strengthening immune functions. However, little is known on the molecular processes responsible for the production of these compounds. This is partly due to the absence of genomic resources, such as sequences of key enzyme genes in the biosynthetic pathways. In the present study, the transcriptome of C. officinalis was analyzed by the RNA sequencing. A total of 54,827 unigenes were yielded by de novo assembly, of which 31,780 unigenes were successfully annotated. As potential molecular markers, 121, 118, 96, 89, and 82 transcription factors belonged to bHLH, MYB, PHD, WRKY, and AP2-ERF were obtained, respectively. Moreover, the results showing that geraniol 10-hydroxylase (G10H) and secologanin synthase (SLS) were differentially expressed in fruits and leaves during different growing stages were confirmed by qRT-PCR. Furthermore, we identified two distinct expression patterns of G10H and SLS in loganin synthesis of C. officinalis fruits. Collectively, the genomic information and gene expression results presented in this study will be helpful for future studies on gene discovery and molecular process of loganin synthesis in C. officinalis.
KeywordsCornus officinalis Loganin Transcriptome RNA-seq
We thank Drs. Yinghua Zha and Lei Zhang for their helpful revision on this manuscript. We thank Drs. Robin Buell and Dongyan Zhao for their kind assistance on genome sequences. We also thank Professor Vincent Courdavault for the technical support on the figures. This work was supported by the Innovation Team Project of Breeding and Standardized Production of New Varieties of Traditional Chinese Medicine in Fundamental Research Funds of the Central Universities [GK201801008 to CKB], the National Natural Science Foundation of China [31100241 to CKB], and the Fundamental Research Funds for the Central Universities [GK201503046 to GSL].
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Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
Data archiving statement
The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al. 2002) and are accessible through GEO Series accession number GSE108216 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108216).
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
- Bai CK, Yu JR, Yu F, Zheng P (2009) Genetic diversity and construction of primary core germplasm in Cornus offcinalis by ISSR marker. Acta Botan Boreali-Occiden Sin 29:2401–2407Google Scholar
- Cao B, Bai CK, Zhang LL, Li GS, Mao MC (2016) Modeling habitat distribution of Cornus officinalis with Maxent modeling and fuzzy logics in China. J Plant Ecol 9: 1–12Google Scholar
- Dugé de Bernonville T, Foureau E, Parage C, Lanoue A, Clastre M, Londono MA, Oudin A, Houillé B, Papon N, Besseau S, Glévarec G, Atehortùa L, Giglioli-Guivarc’h N, St-Pierre B, de Luca V, O’Connor SE, Courdavault V (2015) Characterization of a second secologanin synthase isoform producing both secologanin and secoxyloganin allows enhanced de novo assembly of a Catharanthus roseus transcriptome. BMC Genomics 16:619CrossRefPubMedPubMedCentralGoogle Scholar
- Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRefPubMedPubMedCentralGoogle Scholar
- Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512CrossRefPubMedGoogle Scholar
- Hsu E (2008) The history of Chinese medicine in the People’s Republic of China and its globalization. East Asian Science, Technology and Society An International Journal 2:465–484Google Scholar
- Miettinen K, Dong L, Navrot N, Schneider T, Burlat V, Pollier J, Woittiez L, van der Krol S, Lugan R, Ilc T, Verpoorte R, Oksman-Caldentey KM, Martinoia E, Bouwmeester H, Goossens A, Memelink J, Werck-Reichhart D (2014) The seco-iridoid pathway from Catharanthus roseus. Nat Commun 5:3606CrossRefPubMedPubMedCentralGoogle Scholar
- National Pharmacopoeia Committee (2005) Pharmacopoeia of the People’s Republic of China. Chemical Industry Press, BeijingGoogle Scholar