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The genomic basis of the plant island syndrome in Darwin’s giant daisies

Author

Listed:
  • José Cerca

    (Norwegian University of Science and Technology)

  • Bent Petersen

    (University of Copenhagen
    AIMST University)

  • José Miguel Lazaro-Guevara

    (University of British Columbia)

  • Angel Rivera-Colón

    (University of Illinois at Urbana-Champaign)

  • Siri Birkeland

    (Norwegian University of Life Sciences
    University of Oslo)

  • Joel Vizueta

    (University of Copenhagen, Universitetsparken 15)

  • Siyu Li

    (University of California, Davis)

  • Qionghou Li

    (University of British Columbia)

  • João Loureiro

    (University of Coimbra, Calçada Martim de Freitas)

  • Chatchai Kosawang

    (University of Copenhagen)

  • Patricia Jaramillo Díaz

    (Fundación Charles Darwin
    University of Malaga)

  • Gonzalo Rivas-Torres

    (Universidad San Francisco de Quito USFQ
    Galapagos Science Center, USFQ, UNC Chapel Hill
    Universidad San Francisco de Quito USFQ
    University of Florida)

  • Mario Fernández-Mazuecos

    (Universidad Autónoma de Madrid)

  • Pablo Vargas

    (Real Jardín Botánico (RJB-CSIC))

  • Ross A. McCauley

    (Fort Lewis College)

  • Gitte Petersen

    (Stockholm University)

  • Luisa Santos-Bay

    (University of Copenhagen)

  • Nathan Wales

    (University of York)

  • Julian M. Catchen

    (University of Illinois at Urbana-Champaign)

  • Daniel Machado

    (Norwegian University of Science and Technology)

  • Michael D. Nowak

    (University of Oslo)

  • Alexander Suh

    (University of East Anglia, Norwich Research Park
    Uppsala University)

  • Neelima R. Sinha

    (University of California, Davis)

  • Lene R. Nielsen

    (University of Copenhagen)

  • Ole Seberg

    (University of Copenhagen)

  • M. Thomas P. Gilbert

    (Norwegian University of Science and Technology
    University of Copenhagen)

  • James H. Leebens-Mack

    (University of Georgia)

  • Loren H. Rieseberg

    (University of British Columbia)

  • Michael D. Martin

    (Norwegian University of Science and Technology)

Abstract

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies.

Suggested Citation

  • José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31280-w
    DOI: 10.1038/s41467-022-31280-w
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