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

• Published in: Genes & genomics Vol. 42; no. 9; pp. 1011 - 1021
• Main Authors: Roy, Neha Samir, Lee, In-hye, Kim, Jung-A, Ramekar, Rahul Vasudeo, Park, Kyong-Cheul, Park, Nam-il, Yeo, Joo-Hong, Choi, Ik-Young, Kim, Soonok
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01.09.2020; Springer Nature B.V; 한국유전학회
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Biosynthesis; Diabetes mellitus; Euphorbia; Flowers; Gene expression; Genomes; Herbal medicine; Human Genetics; Life Sciences; Medicinal plants; Metabolites; Microbial Genetics and Genomics; Open reading frames; Plant Genetics and Genomics; Research Article; Transcription factors; 생물학; Secondary metabolites; Transcription factors; Illumina HiSeq2000; Unigenes; Transcriptome
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/s13258-020-00957-1

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.