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KMID : 0381120200420091011
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Genes and Genomics
2020 Volume.42 No. 9 p.1011 ~ p.1021
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De novo assembly and characterization of transcriptome in the medicinal plant Euphorbia jolkini
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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 Soon-Ok
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Abstract
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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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KEYWORD
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Euphorbia jolkini, Illumina HiSeq2000, Unigenes, Transcriptome, Secondary metabolites, Transcription factors
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