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Genomics. 2018 Jul 10. pii: S0888-7543(18)30162-9. doi: 10.1016/j.ygeno.2018.06.004. [Epub ahead of print]

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

Author information

1
Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea. Electronic address: jakimhj12@gmail.com.
2
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, South Korea; Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, South Korea. Electronic address: neha_roy@kangwon.ac.kr.
3
Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea. Electronic address: hare0070@gmail.com.
4
DNACare Genomics Institute, Seongnam 13558, South Korea. Electronic address: ahyoung@phyzen.com.
5
Phyzen Genomics Institute, Seongnam 13558, South Korea. Electronic address: bschoi@phyzen.com.
6
DNACare Genomics Institute, Seongnam 13558, South Korea. Electronic address: yeisooyu@phyzen.com.
7
Department of Plant Science, Gangneung Wonju National University, Gangneung 25457, South Korea. Electronic address: nipark@kwnu.ac.kr.
8
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, South Korea. Electronic address: kyongcheul.park@kangwon.ac.kr.
9
Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea. Electronic address: sokim90@korea.kr.
10
Biological Resources Assessment Division, National Institute of Biological Resources, Incheon, Republic of Korea. Electronic address: moeicdy@korea.kr.
11
Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, South Korea. Electronic address: choii@kangwon.ac.kr.

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.

KEYWORDS:

CYP450; Isoforms; Pacbio; Transcriptome; Zanthoxylum planispinum

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