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| Status |
Public on Jul 01, 2018 |
| Title |
De novo transcriptome assembly and characterization of medicinal plant Lithospermum officinale to discover putative genes involved in specialized metabolites biosynthesis |
| Organism |
Lithospermum officinale |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study, we have performed Illumina based RNA sequencing to characterize the transcriptome and expression profiles of genes expressed in 3 tissues of L. officinale. RNA sequencing and de novo transcriptome assembly of L. officinale resulted in a total of 77,047 unigenes with N50 value as 1524 bps. KEGG pathway and GO enrichment analysis using highly expressed unigenes across three tissues showed active secondary metabolic processes specifically enriched to the root of L. officinale. Expression of identified candidate unigenes for specialized metabolites biosynthesis were consistent with previous reports on accumulation of metabolites across different tissues of L. officinale.
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| Overall design |
Examination of 3 tissues of Lithospermum offcinale using Illumina Hi Seq 2000 platform, paired-end, average sequence length as 101bps
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| Contributor(s) |
Yamazaki M, Saito K, Suzuki H, Nakamura M, Rai M, Shimizu Y, Nakaya T, Rai A |
| Citation missing |
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| Submission date |
Mar 02, 2018 |
| Last update date |
Jul 03, 2018 |
| Contact name |
Mami Yamazaki |
| E-mail(s) |
mamiy@faculty.chiba-u.jp
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| Organization name |
Chiba University
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| Department |
Graduate School of Pharmaceutical Sciences
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| Lab |
Department of Molecular Biology and Biotechnology
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| Street address |
Inohana 1-8-1, Chuo-ku
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| City |
Chiba |
| ZIP/Postal code |
2608675 |
| Country |
Japan |
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| Platforms (1) |
| GPL24683 |
Illumina HiSeq 2000 (Lithospermum officinale) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA436733 |
| SRA |
SRP133843 |
