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

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

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

机译：使用单分子直接RNA测序方法的药用植物Zanthoxylum PlanispiniN的基因组转录组分析

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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.

机译：高通量RNA测序已彻底改变了基于转录的候选基因研究，非模型生物中的基于候选基因的研究，关键途径和基因调控。我们分析了Zanthoxylum Planispinum（Z.Parenispinum）的全长cDNA序列，在东亚主要部分的药草中。使用PACBIO RSII平台对叶片，早期果实和成熟果汁阶段的组织衍生的全长mRNA进行测序，以鉴定同种型转录组。我们获得了51,402个unigenes，每种基因平均为1781磅，基因长度为82.473 Mb。在51,402中，3963个unigenes显示各种同种型。通过在各种同种型中的每一个中选择一个代表性基因，我们最终确定了该草本植物的46,306个独特的基因。我们鉴定了76个细胞色素P450（CYP450）和相关的同种型，其在分子功能和生物过程中具有广泛的多样性。这些转录组数据的Z.Planispinum将提供一种良好的资源，以研究制作有价值的药物和植物化学物质的代谢工程。

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《Genomics》 |2019年第4期|共7页
作者
Kim Jung-A; Roy Neha Samir; Lee Inn-hye; Choi Ah-Young; Choi Beom-Soon; Yu Yei-Soo; Park Nam-il; Park Kyong-Cheul; Kim Soonok; Yang Hee-sun; Choi Ik-Young;
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作者单位

Natl Inst Biol Resources Biol Resources Assessment Div Incheon South Korea;

Kangwon Natl Univ Dept Agr &

Life Ind Chunchon 24341 South Korea;

Natl Inst Biol Resources Biol Resources Assessment Div Incheon South Korea;

DNACare Genom Inst Seongnam 13558 South Korea;

Phyzen Genom Inst Seongnam 13558 South Korea;

DNACare Genom Inst Seongnam 13558 South Korea;

Gangneung Wonju Natl Univ Dept Plant Sci Kangnung 25457 South Korea;

Kangwon Natl Univ Dept Agr &

Life Ind Chunchon 24341 South Korea;

Natl Inst Biol Resources Biol Resources Assessment Div Incheon South Korea;

Natl Inst Biol Resources Biol Resources Assessment Div Incheon South Korea;

Kangwon Natl Univ Dept Agr &

Life Ind Chunchon 24341 South Korea;

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原文格式 PDF
正文语种 eng
中图分类医学遗传学;
关键词
CYP450; Isoforms; Pacbio; Transcriptome; Zanthoxylum planispinum;

机译：CYP450;同种型;PACBIO;转录组;Zanthoxylum Planispinum;

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1. Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach [J] . Kim Jung-A, Roy Neha Samir, Lee Inn-hye, Genomics . 2019,第4期

机译：使用单分子直接RNA测序方法的药用植物Zanthoxylum PlanispiniN的基因组转录组分析
2. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis [J] . Qingshan Xu, Junyan Zhu, Shiqi Zhao, Frontiers in Plant Science . 2017,第12期

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3. Comparative Transcriptome Profiling of Disruptive Technology, Single-Molecule Direct RNA Sequencing [J] . Current Bioinformatics . 2020,第2期

机译：具有破坏性技术的比较转录组分析，单分子直接RNA测序
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5. Flow-sorting of Hodgkin Reed-Sternberg cells, low-input sequencing, and bioinformatic profiling: Methodological development and characterization of cancer exomes and transcriptomes [D] . Reichel, Jonathan B. 2015

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6. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis [O] . Qingshan Xu, Junyan Zhu, Shiqi Zhao, -1

机译：转录组分析使用单分子直接RNA测序方法深入了解山茶次生代谢途径中的基因
7. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis [O] . Qingshan Xu, Junyan Zhu, Shiqi Zhao, 2017

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

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