De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini
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Genes & Genomics https://doi.org/10.1007/s13258-020-00957-1
RESEARCH ARTICLE
De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini Neha Samir Roy1,2 · In‑hye Lee3 · Jung‑A Kim3 · Rahul Vasudeo Ramekar1,2 · Kyong‑Cheul Park1 · Nam‑il Park4 · Joo‑Hong Yeo3 · Ik‑Young Choi1,2 · Soonok Kim4 Received: 1 January 2020 / Accepted: 28 May 2020 © The Genetics Society of Korea 2020
Abstract Background Euphorbia jolkini, a medicinal herb that grows on the warm beaches in Japan and South Korea, is known to be used for traditional medicines to treat a variety of ailments, including bruises, stiffness, indigestion, toothache, and diabetes. Objective It is to analyze the whole transcriptome and identify the genes related to the phenylpropanoid biosynthesis in the medicinally important herb E jolkini. Methods Paired-end Illumina HiSeq™ 2500 sequencing technology was employed for cDNA library construction and Illumina sequencing. Public databases like TAIR (The Arabidopsis Information Resource), Swissprot and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used for annotations of unigenes obtained. Results The transcriptome of E. jolkini generated 139,215 assembled transcripts with an average length of 868 bp and an N50 value of 1460 bp that were further clustered using CD-HIT into 93,801 unigenes with an average length of 847 bp (N501410 bp). Sixty-three percent of the coding sequences (CDS) were annotated from the longest open reading frame (ORF). A remarkable percentage of unigenes were annotated against various databases. The differentially expressed gene analysis revealed that the expression of genes related to the terpenoid backbone biosynthesis pathway was higher in the flowers, whereas that of genes related to the phenylpropanoid biosynthesis pathway was both up- and downregulated in flowers and leaves. A search of against the transcription factor domain found 1023 transcription factors (TFs) that were from 54 TF families. Conclusion Assembled sequences of the E. jolkini transcriptome are made available for the first time in this study E. jolkini and lay a foundation for the investigation of secondary metabolite biosynthesis. Keywords Euphorbia jolkini · Illumina HiSeq2000 · Unigenes · Transcriptome · Secondary metabolites · Transcription factors Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00957-1) contains supplementary material, which is available to authorized users. * Ik‑Young Choi [email protected]
Nam‑il Park [email protected]
* Soonok Kim [email protected]
Joo‑Hong Yeo [email protected]
Neha Samir Roy [email protected]
1
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Republic of Korea
2
Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
3
Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea
4
Department o
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