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AbdAlla HAM, Wanga VO, Mkala EM, Amenu SG, Amar MH, Chen L, Wang QF. Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order. Front Genet 2023; 14:1131644. [PMID: 36992699 PMCID: PMC10040795 DOI: 10.3389/fgene.2023.1131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Moringa is a mono-genus belonging to the Moringaceae family, which includes 13 species. Among them, Moringa peregrina is plant species native to the Arabian Peninsula, Southern Sinai in Egypt, and the Horn of Africa, and comprehensive studies on its nutritional, industrial, and medicinal values have been performed. Herein, we sequenced and analyzed the initial complete chloroplast genome of Moringa peregrina. Concurrently, we analyzed the new chloroplast genome along with 25 chloroplast genomes related to species representing eight families in the Brassicales order. The results indicate that the plastome sequence of M. peregrina consists of 131 genes, with an average GC content of 39.23%. There is a disparity in the IR regions of the 26 species ranging from 25,804 to 31,477 bp. Plastome structural variations generated 20 hotspot regions that could be considered prospective DNA barcode locations in the Brassicales order. Tandem repeats and SSR structures are reported as significant evidence of structural variations among the 26 tested specimens. Furthermore, selective pressure analysis was performed to estimate the substitution rate within the Moringaceae family, which revealing that the ndhA and accD genes are under positive selective pressure. The phylogenetic analysis of the Brassicales order produced an accurate monophyletic annotation cluster of the Moringaceae and Capparaceae species, offering unambiguous identification without overlapping groups between M. oleifera and M. peregrina, which are genetically strongly associated. Divergence time estimation suggests that the two Moringa species recently diversified, 0.467 Ma. Our findings highlight the first complete plastome of the Egyptian wild-type of M. peregrina, which can be used for determining plastome phylogenetic relationships and systematic evolution history within studies on the Moringaceae family.
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Affiliation(s)
- Heba A. M. AbdAlla
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Botany Department, Agriculture and Biological Institute, National Research Centre, Giza, Egypt
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Sara Getachew Amenu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed Hamdy Amar
- Egyptian Deserts Gene Bank, Desert Research Center, Cairo, Egypt
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Lingyun Chen
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
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