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The genome and transcriptome analysis of the vigna mungo chloroplast
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Document Title
The genome and transcriptome analysis of the vigna mungo chloroplast
Author
Nawae W., Yundaeng C., Naktang C., Kongkachana W., Yoocha T., Sonthirod C., Narong N., Somta P., Laosatit K., Tangphatsornruang S., Pootakham W.
Name from Authors Collection
Scopus Author ID
57201312649
Scopus Author ID
56030033100
Scopus Author ID
57219199429
Affiliations
National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart UniversityNakhon Pathom 73140, Thailand
Type
Article
Source Title
Plants
ISSN
22237747
Year
2020
Volume
9
Issue
9
Page
42736
Open Access
All Open Access, Gold, Green
Publisher
MDPI AG
DOI
10.3390/plants9091247
Format
Abstract
Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51‐kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G‐to‐A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine‐rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G‐to‐A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering. © 2020, MDPI AG. All rights reserved.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
National Science and Technology Development Agency
Funding Number
1000221
License
CC BY
Rights
N/A
Publication Source
Scopus