Comparative genomics provides insights into the biogeographic and biochemical diversity of meliaceous species

Jia Liu, Zhennan Wang, Xinyao Su, Liang Leng, Jiarou Liu, Feng Zhang, Shilin Chen (), Yujun Zhang () and Caixia Wang ()
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Jia Liu: China Academy of Chinese Medical Sciences
Zhennan Wang: China Academy of Chinese Medical Sciences
Xinyao Su: China Academy of Chinese Medical Sciences
Liang Leng: Chengdu University of Traditional Chinese Medicine
Jiarou Liu: China Academy of Chinese Medical Sciences
Feng Zhang: China Academy of Chinese Medical Sciences
Shilin Chen: China Academy of Chinese Medical Sciences
Yujun Zhang: China Academy of Chinese Medical Sciences
Caixia Wang: China Academy of Chinese Medical Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Meliaceous plants such as Azadirachta indica (neem) and Melia azedarach (chinaberry) contain large amounts of limonoids with unique anti-insect activities. However, genes responsible for downstream modifications of limonoids are not well known. Here, we improve the genome assemblies of neem and chinaberry to the telomere-to-telomere (T2T) level. Allopatric speciation of the two plants is confirmed by the lineage-specific inversion of chromosome 12 in the neem lineage. We further identify two BAHD-acetyltransferases (ATs) in chinaberry (MaAT8824 and MaAT1704) that catalyse acetylation at both the C-12 and C-3 hydroxyl groups of limonoids, whereas the syntenic neem copy (AiAT0635) does not possess this activity. A critical N-terminal region (SAGAVP) is crucial for the acetylation of AiAT0635, and swapping it into the MaAT8824 version (CHRSSG) can endow it with acetylation activity. Our improved genome assemblies provide insights into allopatric speciation of neem, as well as limonoid biosynthesis and chemical diversity in meliaceous plants.

Date: 2025
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DOI: 10.1038/s41467-025-57722-9

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