The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast
<i>Vigna mungo</i> 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 <i>V. mungo</i> chloroplast. We identified many positively...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-09-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/9/1247 |
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| author | Wanapinun Nawae Chutintorn Yundaeng Chaiwat Naktang Wasitthee Kongkachana Thippawan Yoocha Chutima Sonthirod Nattapol Narong Prakit Somta Kularb Laosatit Sithichoke Tangphatsornruang Wirulda Pootakham |
| author_facet | Wanapinun Nawae Chutintorn Yundaeng Chaiwat Naktang Wasitthee Kongkachana Thippawan Yoocha Chutima Sonthirod Nattapol Narong Prakit Somta Kularb Laosatit Sithichoke Tangphatsornruang Wirulda Pootakham |
| author_sort | Wanapinun Nawae |
| collection | DOAJ |
| description | <i>Vigna mungo</i> 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 <i>V. mungo</i> chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., <i>rbcL</i>, <i>ndhF</i>, and <i>atpF</i>) and RNA polymerase genes (e.g., <i>rpoC2</i>) from the comparison of the chloroplast genome of <i>V. mungo</i>, 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 <i>accD</i> polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of <i>clpP</i> in the leaf, shoot, flower, fruit, and root tissues of <i>V. mungo</i>. 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 <i>ycf4</i> gene. The edited guanine bases were found particularly in the chloroplast genome of the <i>Vigna</i> species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The <i>V. mungo</i> chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering. |
| first_indexed | 2024-03-10T16:09:32Z |
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| id | doaj.art-3f786565d25d4709b61257c71c46c9e4 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T16:09:32Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-3f786565d25d4709b61257c71c46c9e42023-11-20T14:34:05ZengMDPI AGPlants2223-77472020-09-0199124710.3390/plants9091247The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> ChloroplastWanapinun Nawae0Chutintorn Yundaeng1Chaiwat Naktang2Wasitthee Kongkachana3Thippawan Yoocha4Chutima Sonthirod5Nattapol Narong6Prakit Somta7Kularb Laosatit8Sithichoke Tangphatsornruang9Wirulda Pootakham10National Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandDepartment of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, ThailandDepartment of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Omics Center (NOC), National Science and Technology Development Agency, 111 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand<i>Vigna mungo</i> 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 <i>V. mungo</i> chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., <i>rbcL</i>, <i>ndhF</i>, and <i>atpF</i>) and RNA polymerase genes (e.g., <i>rpoC2</i>) from the comparison of the chloroplast genome of <i>V. mungo</i>, 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 <i>accD</i> polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of <i>clpP</i> in the leaf, shoot, flower, fruit, and root tissues of <i>V. mungo</i>. 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 <i>ycf4</i> gene. The edited guanine bases were found particularly in the chloroplast genome of the <i>Vigna</i> species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The <i>V. mungo</i> chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.https://www.mdpi.com/2223-7747/9/9/1247chloroplast genomechloroplast transcriptomelegume<i>Vigna mungo</i>comparative analysispositive selection |
| spellingShingle | Wanapinun Nawae Chutintorn Yundaeng Chaiwat Naktang Wasitthee Kongkachana Thippawan Yoocha Chutima Sonthirod Nattapol Narong Prakit Somta Kularb Laosatit Sithichoke Tangphatsornruang Wirulda Pootakham The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast Plants chloroplast genome chloroplast transcriptome legume <i>Vigna mungo</i> comparative analysis positive selection |
| title | The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast |
| title_full | The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast |
| title_fullStr | The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast |
| title_full_unstemmed | The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast |
| title_short | The Genome and Transcriptome Analysis of the <i>Vigna mungo</i> Chloroplast |
| title_sort | genome and transcriptome analysis of the i vigna mungo i chloroplast |
| topic | chloroplast genome chloroplast transcriptome legume <i>Vigna mungo</i> comparative analysis positive selection |
| url | https://www.mdpi.com/2223-7747/9/9/1247 |
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