IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-53157-w.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-53157-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-53157-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Xiao Feng & Qipian Chen & Weihong Wu & Jiexin Wang & Guohong Li & Shaohua Xu & Shao Shao & Min Liu & Cairong Zhong & Chung-I Wu & Suhua Shi & Ziwen He, 2024. "Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Robert VanBuren & Ching Man Wai & Xuewen Wang & Jeremy Pardo & Alan E. Yocca & Hao Wang & Srinivasa R. Chaluvadi & Guomin Han & Douglas Bryant & Patrick P. Edger & Joachim Messing & Mark E. Sorrells &, 2020. "Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    3. Xiaohan Yang & Rongbin Hu & Hengfu Yin & Jerry Jenkins & Shengqiang Shu & Haibao Tang & Degao Liu & Deborah A. Weighill & Won Cheol Yim & Jungmin Ha & Karolina Heyduk & David M. Goodstein & Hao-Bo Guo, 2017. "The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism," Nature Communications, Nature, vol. 8(1), pages 1-15, December.
    4. Gerald S. Wilkinson & Danielle M. Adams & Amin Haghani & Ake T. Lu & Joseph Zoller & Charles E. Breeze & Bryan D. Arnold & Hope C. Ball & Gerald G. Carter & Lisa Noelle Cooper & Dina K. N. Dechmann & , 2021. "DNA methylation predicts age and provides insight into exceptional longevity of bats," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. Nanqiao Liao & Zhongyuan Hu & Jinshan Miao & Xiaodi Hu & Xiaolong Lyu & Haitian Fang & Yi-Mei Zhou & Ahmed Mahmoud & Guancong Deng & Yi-Qing Meng & Kejia Zhang & Yu-Yuan Ma & Yuelin Xia & Meng Zhao & , 2022. "Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Gerald S. Wilkinson & Danielle M. Adams & Amin Haghani & Ake T. Lu & Joseph Zoller & Charles E. Breeze & Bryan D. Arnold & Hope C. Ball & Gerald G. Carter & Lisa Noelle Cooper & Dina K. N. Dechmann & , 2021. "Author Correction: DNA methylation predicts age and provides insight into exceptional longevity of bats," Nature Communications, Nature, vol. 12(1), pages 1-2, December.
    7. Tao Wan & Zhiming Liu & Ilia J. Leitch & Haiping Xin & Gillian Maggs-Kölling & Yanbing Gong & Zhen Li & Eugene Marais & Yiying Liao & Can Dai & Fan Liu & Qijia Wu & Chi Song & Yadong Zhou & Weichang H, 2021. "The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    8. Andrew H. Paterson & Jonathan F. Wendel & Heidrun Gundlach & Hui Guo & Jerry Jenkins & Dianchuan Jin & Danny Llewellyn & Kurtis C. Showmaker & Shengqiang Shu & Joshua Udall & Mi-jeong Yoo & Robert Bye, 2012. "Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres," Nature, Nature, vol. 492(7429), pages 423-427, December.
    9. Wei Liu & Giovanni Giuriani & Anezka Havlikova & Dezhi Li & Douglas J. Lamont & Susanne Neugart & Christos N. Velanis & Jan Petersen & Ute Hoecker & John M. Christie & Gareth I. Jenkins, 2024. "Phosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Adriana Arneson & Amin Haghani & Michael J. Thompson & Matteo Pellegrini & Soo Bin Kwon & Ha Vu & Emily Maciejewski & Mingjia Yao & Caesar Z. Li & Ake T. Lu & Marco Morselli & Liudmilla Rubbi & Bret B, 2022. "A mammalian methylation array for profiling methylation levels at conserved sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Steve Horvath & Joshua Zhang & Amin Haghani & Ake T. Lu & Zhe Fei, 2024. "Fundamental equations linking methylation dynamics to maximum lifespan in mammals," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Zhen-Hui Wang & Xin-Feng Wang & Tianyuan Lu & Ming-Rui Li & Peng Jiang & Jing Zhao & Si-Tong Liu & Xue-Qi Fu & Jonathan F. Wendel & Yves Peer & Bao Liu & Lin-Feng Li, 2022. "Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Otto, Moritz & Wiehe, Thomas, 2023. "The structured coalescent in the context of gene copy number variation," Theoretical Population Biology, Elsevier, vol. 154(C), pages 67-78.
    5. Salman Naveed & Sachin Rustgi, 2023. "Functional Characterization of Candidate Genes, Gohir.D05G103700 and Gohir.D12G153600 , Identified through Expression QTL Analysis Using Virus-Induced Gene Silencing in Upland Cotton ( Gossypium hirsu," Agriculture, MDPI, vol. 13(5), pages 1-12, May.
    6. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    7. Man Xing & Bo Hong & Mengjie Lv & Xueyi Lan & Danhui Zhang & Chunlei Shu & Shucheng Qi & Zechuan Peng & Chunyun Guan & Xinghua Xiong & Luyao Huang, 2024. "Analysis of BnGPAT9 Gene Expression Patterns in Brassica napus and Its Impact on Seed Oil Content," Agriculture, MDPI, vol. 14(8), pages 1-18, August.
    8. Xiao-Xiao Wang & Chien-Hsun Huang & Diego F. Morales-Briones & Xiang-Yu Wang & Ying Hu & Na Zhang & Pu-Guang Zhao & Xiao-Mei Wei & Kun-Hua Wei & Xinya Hemu & Ning-Hua Tan & Qing-Feng Wang & Ling-Yun C, 2024. "Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    10. Junhui Yuan & Sanjie Jiang & Jianbo Jian & Mingyu Liu & Zhen Yue & Jiabao Xu & Juan Li & Chunyan Xu & Lihong Lin & Yi Jing & Xiaoxiao Zhang & Haixin Chen & Linjuan Zhang & Tao Fu & Shuiyan Yu & Zhangy, 2022. "Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    11. Heqiang Lou & Lili Song & Xiaolong Li & Hailing Zi & Weijie Chen & Yadi Gao & Shan Zheng & Zhangjun Fei & Xuepeng Sun & Jiasheng Wu, 2023. "The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    12. Oluwaseyi Shorinola & Rose Marks & Peter Emmrich & Chris Jones & Damaris Odeny & Mark A. Chapman, 2024. "Integrative and inclusive genomics to promote the use of underutilised crops," Nature Communications, Nature, vol. 15(1), pages 1-4, December.
    13. Min-Rui-Xuan Xu & Zhen-Yang Liao & Jordan R. Brock & Kang Du & Guo-Yin Li & Zhi-Qiang Chen & Ying-Hao Wang & Zhong-Nan Gao & Gaurav Agarwal & Kevin H-C Wei & Feng Shao & Shuai Pang & Adrian E. Platts , 2023. "Maternal dominance contributes to subgenome differentiation in allopolyploid fishes," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    14. David Wickell & Li-Yaung Kuo & Hsiao-Pei Yang & Amra Dhabalia Ashok & Iker Irisarri & Armin Dadras & Sophie de Vries & Jan de Vries & Yao-Moan Huang & Zheng Li & Michael S. Barker & Nolan T. Hartwick , 2021. "Underwater CAM photosynthesis elucidated by Isoetes genome," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    15. Katrien M. Devos & Peng Qi & Bochra A. Bahri & Davis M. Gimode & Katharine Jenike & Samuel J. Manthi & Dagnachew Lule & Thomas Lux & Liliam Martinez-Bello & Thomas H. Pendergast & Chris Plott & Dipnar, 2023. "Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53157-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.