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

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, Gonzalo Rivas-Torres, Mario Fernández-Mazuecos, Pablo Vargas, Ross A. McCauley, Gitte Petersen, Luisa Santos-Bay, Nathan Wales, Julian M. Catchen, Daniel Machado, Michael D. Nowak, Alexander Suh, Neelima R. Sinha, Lene R. Nielsen, Ole Seberg, M. Thomas P. Gilbert, James H. Leebens-Mack, Loren H. Rieseberg and Michael D. Martin ()
Additional contact information
José Cerca: Norwegian University of Science and Technology
Bent Petersen: University of Copenhagen
José Miguel Lazaro-Guevara: University of British Columbia
Angel Rivera-Colón: University of Illinois at Urbana-Champaign
Siri Birkeland: Norwegian University of Life Sciences
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
Gonzalo Rivas-Torres: Universidad San Francisco de Quito USFQ
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
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
James H. Leebens-Mack: University of Georgia
Loren H. Rieseberg: University of British Columbia
Michael D. Martin: Norwegian University of Science and Technology

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-31280-w

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