Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

Authors: CHANG, JIYANG - Ghent University; MARCZUK-ROJAS, JUAN - University Of Almeria; WATERMAN, CARRIE - University Of California; GARCIA-LLANOS, ARMANDO - University Of California; CHEN, SHIYU - University Of California; MA, XIAO - Ghent University; Hulse-Kemp, Amanda; VAN DEYNZE, ALLEN - University Of California; VAN DE PEER, YVES - Ghent University; CARRETERO-PAULET, LORENZO - University Of Almeria

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2022
Publication Date: 7/27/2022
Citation: Chang, J., Marczuk-Rojas, J.P., Waterman, C., Garcia-Llanos, A., Chen, S., Ma, X., Hulse-Kemp, A.M., Van Deynze, A., Van De Peer, Y., Carretero-Paulet, L. 2022. Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication. The Plant Genome. https://doi.org/10.1002/tpg2.20238.
DOI: https://doi.org/10.1002/tpg2.20238

Interpretive Summary: Moringa is a highly nutritious, fast-growing and drought-tolerant tree crop in Africa. It was among one of the first 101 plant species identified by the African Orphan Crops Consortium to have its full genetic code assimilated into a full genetic blueprint or genome sequence. Because of its extensive uses and the culture of Moringa, often referred to as a multipurpose tree, we have generated a significantly improved genome sequence. This new resource has enabled us to identify duplications in aspects of its genetic blueprint that are playing a prominent role in important genetic pathways that lead to production of many different compounds in the plant, including flavonoid and alkaloid compounds, as well as the plant’s ability to respond to invading pathogens. This aspect of Moringa's genetic blueprint may partially explain why it can be of such varying use. The improved genome sequence will provide a base for many future studies as well as a guide for plant breeders to provide improved Moringa lines for farmers.

Technical Abstract: The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast-growing, and drought-tolerant tree crop Moringa oleifera (Moringa) as one of the first of 101 plant species to have its genome sequenced and a first draft assembly was published in 2019. Given the extensive uses and culture of Moringa, often referred to as the multipurpose tree, we generated a significantly improved new version of the genome based on long-read sequencing. We leveraged this nearly complete version of the Moringa genome to investigate main drivers of gene family and genome evolution that may be at the origin of relevant biological innovations including agronomical favorable traits. Our results reveal that Moringa has not undergone any additional whole genome duplication (WGD) or polyploidy event beyond the WGD shared by all core eudicots. Moringa duplicates retained following that ancient WGD event are also enriched for functions commonly considered as dosage-balance sensitive. Furthermore, tandem duplications seem to have played a prominent role in the evolution of specific secondary metabolism pathways, including those involved in the biosynthesis of bioactive glucosinolate, flavonoid and alkaloid compounds, as well as of defense response pathways and might partially explain the outstanding phenotypic plasticity attributed to this species. This study provides a genetic roadmap to guide future breeding programs, especially those aimed at improving secondary metabolism related traits in Moringa.