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

Justine K. Kitony, Kelly Colt, Bradley W. Abramson, Nolan T. Hartwick, Semar Petrus, Emadeldin H. E. Konozy, Nisa Karimi, Levi Yant and Todd P. Michael ()
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Justine K. Kitony: The Salk Institute for Biological Studies
Kelly Colt: The Salk Institute for Biological Studies
Bradley W. Abramson: The Salk Institute for Biological Studies
Nolan T. Hartwick: The Salk Institute for Biological Studies
Semar Petrus: The Salk Institute for Biological Studies
Emadeldin H. E. Konozy: University of Cape Coast
Nisa Karimi: Science and Conservation Division
Levi Yant: University of Nottingham
Todd P. Michael: The Salk Institute for Biological Studies

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-53157-w

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