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

Author

Listed:
  • 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
    Inc.)

  • Nolan T. Hartwick

    (The Salk Institute for Biological Studies)

  • Semar Petrus

    (The Salk Institute for Biological Studies
    Cepheid)

  • Emadeldin H. E. Konozy

    (University of Cape Coast)

  • Nisa Karimi

    (Science and Conservation Division
    University of Wisconsin - Madison)

  • Levi Yant

    (University of Nottingham
    Charles University)

  • Todd P. Michael

    (The Salk Institute for Biological Studies)

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.

Suggested Citation

  • Justine K. Kitony & Kelly Colt & Bradley W. Abramson & Nolan T. Hartwick & Semar Petrus & Emadeldin H. E. Konozy & Nisa Karimi & Levi Yant & Todd P. Michael, 2024. "Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53157-w
    DOI: 10.1038/s41467-024-53157-w
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