Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3-11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation.

Biomedical and Clinical Research Centre College of Health and Allied Sciences University of Cape Coast Cape Coast Ghana

Cepheid Sunnyvale CA USA

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Botany University of Wisconsin Madison Madison WI USA

Missouri Botanical Garden Science and Conservation Division St Louis MO USA

Noblis Inc Washington DC USA

Plant Molecular and Cellular Biology Laboratory The Salk Institute for Biological Studies La Jolla CA USA

School of Life Sciences University of Nottingham Nottingham UK

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Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation