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De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini

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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 (N50-1410 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.

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Data availability

The RNA-Seq data in this study were submitted at the NCBI public database under the accession number PRJNA627505 (https://www.ncbi.nlm.nih.gov/sra/PRJNA627505).

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Acknowledgements

This work was supported by the National Institute of Biological resources, Ministry of Environment (MOE) of the Republic of Korea (NIBR201830101, NIBR201921101).

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Authors and Affiliations

  1. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Neha Samir Roy, Rahul Vasudeo Ramekar, Kyong-Cheul Park & Ik-Young Choi

  2. Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Neha Samir Roy, Rahul Vasudeo Ramekar & Ik-Young Choi

  3. Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea

    In-hye Lee, Jung-A Kim & Joo-Hong Yeo

  4. Department of Plant Science, Gangneung Wonju National University, Gangneung, 25457, South Korea

    Nam-il Park & Soonok Kim

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  1. Neha Samir Roy
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Contributions

SK and IYC conceived and designed the project. JK, SK and NIP collected plants and prepared sample materials for genome analysis. IL, JK, JHY, NIP, KCP and NSR performed experiment. RVR, NSR analysed the data. NSR was a major contributor to write the manuscript. SK, KCP and IYC corrected and completed the manuscript.

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Correspondence to Ik-Young Choi or Soonok Kim.

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Roy, N.S., Lee, Ih., Kim, JA. et al. De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini. Genes Genom 42, 1011–1021 (2020). https://doi.org/10.1007/s13258-020-00957-1

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