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| Status |
Public on Jul 17, 2018 |
| Title |
De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis |
| Organism |
Cornus officinalis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cornus officinalis Sieb. et Zucc., a perennial woody plant which is recognized with high medicinal, economic and ecological values, 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 medical properties of this species, owing to the absence of genomic resources such as available sequences of key enzyme genes in biosynthetic pathways. In this study, the RNA sequencing data of C. officinalis were first generated and used for transcriptome analysis. A total of 54,827 unigenes with an average length of 817 bp, an N50 of 1,379 bp, and an average GC content of 44.91% 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 further analyzed, respectively. The results of qRT-PCR confirmed that geraniol 10-hydroxylase (G10H) and loganin synthase (SLS) were differentially expressed in fruits and leaves during different growing stages. Furthermore, we found that loganin accumulation was positively related to G10H expression but was negatively correlated with SLS expression. 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.
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| Overall design |
Fruit mRNA profiles of Cornus officinalis Sieb. et Zucc. collected in June were generated by deep sequencing, in a mixture of three samples, using Illumina® Hiseq 2000 platform.qRT–PCR validation was performed using SYBR Green assays.
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| Contributor(s) |
Bai C, Wu Y, Cao B, Xu J, Li G |
| Citation |
Chengke Bai, Yongmei Wu, Bo Cao, Jun Xu, and Guishuang Li. De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis. Tree Genetics & Genomes 2018;14:57. doi:10.1007/s11295-018-1270-0
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| Submission date |
Dec 18, 2017 |
| Last update date |
Oct 19, 2018 |
| Contact name |
Bo Cao |
| E-mail(s) |
bocao@vip.qq.com
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| Organization name |
Shaanxi Normal University
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| Street address |
620 West Chang'an Road, Changan District
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| City |
Xi'an |
| State/province |
Shaanxi |
| ZIP/Postal code |
710119 |
| Country |
China |
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| Platforms (1) |
| GPL24406 |
Illumina HiSeq 2000 (Cornus officinalis) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA422865 |
| SRA |
SRP126948 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108216_RAW.tar |
4.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE108216_Trinity.fasta.gz |
15.7 Mb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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