Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order
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...
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1131644/full |
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| author | Heba A. M. AbdAlla Heba A. M. AbdAlla Heba A. M. AbdAlla Vincent Okelo Wanga Vincent Okelo Wanga Vincent Okelo Wanga Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Sara Getachew Amenu Sara Getachew Amenu Mohamed Hamdy Amar Lingyun Chen Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_facet | Heba A. M. AbdAlla Heba A. M. AbdAlla Heba A. M. AbdAlla Vincent Okelo Wanga Vincent Okelo Wanga Vincent Okelo Wanga Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Sara Getachew Amenu Sara Getachew Amenu Mohamed Hamdy Amar Lingyun Chen Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_sort | Heba A. M. AbdAlla |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T04:06:44Z |
| format | Article |
| id | doaj.art-d11b474b8c924e7fbc6437c1efaec079 |
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| language | English |
| last_indexed | 2024-04-10T04:06:44Z |
| publishDate | 2023-03-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-d11b474b8c924e7fbc6437c1efaec0792023-03-13T05:24:42ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-03-011410.3389/fgene.2023.11316441131644Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales orderHeba A. M. AbdAlla0Heba A. M. AbdAlla1Heba A. M. AbdAlla2Vincent Okelo Wanga3Vincent Okelo Wanga4Vincent Okelo Wanga5Elijah Mbandi Mkala6Elijah Mbandi Mkala7Elijah Mbandi Mkala8Sara Getachew Amenu9Sara Getachew Amenu10Mohamed Hamdy Amar11Lingyun Chen12Qing-Feng Wang13Qing-Feng Wang14Qing-Feng Wang15CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaPlant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, ChinaBotany Department, Agriculture and Biological Institute, National Research Centre, Giza, EgyptCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaPlant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaPlant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaPlant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, ChinaEgyptian Deserts Gene Bank, Desert Research Center, Cairo, EgyptDepartment of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, ChinaCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaPlant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaMoringa 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.https://www.frontiersin.org/articles/10.3389/fgene.2023.1131644/fullcomparative genomicsendangeredwild egyptian moringa peregrinaplastomephylogenyestimation time |
| spellingShingle | Heba A. M. AbdAlla Heba A. M. AbdAlla Heba A. M. AbdAlla Vincent Okelo Wanga Vincent Okelo Wanga Vincent Okelo Wanga Elijah Mbandi Mkala Elijah Mbandi Mkala Elijah Mbandi Mkala Sara Getachew Amenu Sara Getachew Amenu Mohamed Hamdy Amar Lingyun Chen Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order Frontiers in Genetics comparative genomics endangered wild egyptian moringa peregrina plastome phylogeny estimation time |
| title | Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order |
| title_full | Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order |
| title_fullStr | Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order |
| title_full_unstemmed | Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order |
| title_short | Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order |
| title_sort | comparative genomics analysis of endangered wild egyptian moringa peregrina forssk fiori plastome with implications for the evolution of brassicales order |
| topic | comparative genomics endangered wild egyptian moringa peregrina plastome phylogeny estimation time |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1131644/full |
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