Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order

Heba A M AbdAlla; Vincent Okelo Wanga; Elijah Mbandi Mkala; Sara Getachew Amenu; Mohamed Hamdy Amar; Lingyun Chen; Qing-Feng Wang

doi:10.3389/fgene.2023.1131644

Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order

Front Genet. 2023 Mar 13:14:1131644. doi: 10.3389/fgene.2023.1131644. eCollection 2023.

Authors

Heba A M AbdAlla^{1

2

3}, Vincent Okelo Wanga^{1

2

4}, Elijah Mbandi Mkala^{1

2

4}, Sara Getachew Amenu^{1

2}, Mohamed Hamdy Amar⁵, Lingyun Chen⁶, Qing-Feng Wang^{1

2

4}

Affiliations

¹ CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
² Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China.
³ Botany Department, Agriculture and Biological Institute, National Research Centre, Giza, Egypt.
⁴ Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
⁵ Egyptian Deserts Gene Bank, Desert Research Center, Cairo, Egypt.
⁶ Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China.

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.

Keywords: comparative genomics; endangered; estimation time; phylogeny; plastome; wild egyptian moringa peregrina.

Grants and funding

SHAMA was supported by the CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 4 30074, China and also the Sino-Africa Joint Research Center. This work was funded by the National Natural Science Foundation of China (No. 319611430 and grant number 31670226).