Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants
Within the family Solanaceae, <i>Withania</i> is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of <i>W. coagulans, W. adpressa</i>, and <i>W. riebeckii.</i> The length of these genomes rang...
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MDPI AG
2020-06-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/6/752 |
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| author | Furrukh Mehmood Abdullah Zartasha Ubaid Yiming Bao Peter Poczai Bushra Mirza |
| author_facet | Furrukh Mehmood Abdullah Zartasha Ubaid Yiming Bao Peter Poczai Bushra Mirza |
| author_sort | Furrukh Mehmood |
| collection | DOAJ |
| description | Within the family Solanaceae, <i>Withania</i> is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of <i>W. coagulans, W. adpressa</i>, and <i>W. riebeckii.</i> The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635–85,765 bp and a small single-copy (SSC) region of 18,457–18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of <i>Withania</i> plastomes, which revealed high similarities among the species. Comparative analysis among the <i>Withania</i> species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (<i>rps</i>4-<i>trn</i>T, <i>trn</i>M-<i>atp</i>E, and <i>rps</i>15) were sufficient to discriminate the <i>Withania</i> species included in current study. |
| first_indexed | 2024-03-10T19:09:37Z |
| format | Article |
| id | doaj.art-dca5fedc4466496b834434daf6015d70 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T19:09:37Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-dca5fedc4466496b834434daf6015d702023-11-20T03:54:50ZengMDPI AGPlants2223-77472020-06-019675210.3390/plants9060752Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal PlantsFurrukh Mehmood0Abdullah1Zartasha Ubaid2Yiming Bao3Peter Poczai4Bushra Mirza5Department of Biochemistry, Quaid-i-Azam University, Islamabad 45320, PakistanDepartment of Biochemistry, Quaid-i-Azam University, Islamabad 45320, PakistanDepartment of Biochemistry, Quaid-i-Azam University, Islamabad 45320, PakistanNational Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, ChinaBotany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, FinlandDepartment of Biochemistry, Quaid-i-Azam University, Islamabad 45320, PakistanWithin the family Solanaceae, <i>Withania</i> is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of <i>W. coagulans, W. adpressa</i>, and <i>W. riebeckii.</i> The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635–85,765 bp and a small single-copy (SSC) region of 18,457–18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of <i>Withania</i> plastomes, which revealed high similarities among the species. Comparative analysis among the <i>Withania</i> species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (<i>rps</i>4-<i>trn</i>T, <i>trn</i>M-<i>atp</i>E, and <i>rps</i>15) were sufficient to discriminate the <i>Withania</i> species included in current study.https://www.mdpi.com/2223-7747/9/6/752ashwagandhachloroplast genomeindelsmedicinal plantsmutational hotspotsphylogenomics |
| spellingShingle | Furrukh Mehmood Abdullah Zartasha Ubaid Yiming Bao Peter Poczai Bushra Mirza Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants Plants ashwagandha chloroplast genome indels medicinal plants mutational hotspots phylogenomics |
| title | Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants |
| title_full | Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants |
| title_fullStr | Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants |
| title_full_unstemmed | Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants |
| title_short | Comparative Plastomics of Ashwagandha (<i>Withania</i>, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants |
| title_sort | comparative plastomics of ashwagandha i withania i solanaceae and identification of mutational hotspots for barcoding medicinal plants |
| topic | ashwagandha chloroplast genome indels medicinal plants mutational hotspots phylogenomics |
| url | https://www.mdpi.com/2223-7747/9/6/752 |
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