Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach

Jung A. Kim, Neha Samir Roy, Inn hye Lee, Ah Young Choi, Beom Soon Choi, Yei Soo Yu, Nam il Park, Kyong Cheul Park, Soonok Kim, Hee sun Yang, Ik Young Choi

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

High-throughput RNA sequencing has revolutionized transcriptome-based studies of candidate genes, key pathways and gene regulation in non-model organisms. We analyzed full-length cDNA sequences in Zanthoxylum planispinum (Z. planispinum), a medicinal herb in major parts of East Asia. The full-length mRNA derived from tissues of leaf, early fruit and maturing fruit stage were sequenced using PacBio RSII platform to identify isoform transcriptome. We obtained 51,402 unigenes, with average 1781 bp per gene in 82.473 Mb gene lengths. Among 51,402, 3963 unigenes showed variety of isoform. By selection of one representative gene among each of the various isoforms, we finalized 46,306 unique gene set for this herb. We identified 76 cytochrome P450 (CYP450) and related isoforms that are of the wide diversity in the molecular function and biological process. These transcriptome data of Z. planispinum will provide a good resource to study metabolic engineering for the production of valuable medicinal drugs and phytochemicals.

Original languageEnglish (US)
Pages (from-to)973-979
Number of pages7
JournalGenomics
Volume111
Issue number4
DOIs
StatePublished - Jul 2019

Keywords

  • CYP450
  • Isoforms
  • Pacbio
  • Transcriptome
  • Zanthoxylum planispinum

ASJC Scopus subject areas

  • Genetics

Fingerprint

Dive into the research topics of 'Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach'. Together they form a unique fingerprint.

Cite this