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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

The genomic basis of the plant island syndrome in Darwin’s giant daisies. / Cerca, José; Petersen, Bent; Lazaro-Guevara, José Miguel; Rivera-Colón, Angel; Birkeland, Siri; Vizueta, Joel; Li, Siyu; Li, Qionghou; Loureiro, João; Kosawang, Chatchai; Díaz, Patricia Jaramillo; Rivas-Torres, Gonzalo; Fernández-Mazuecos, Mario; Vargas, Pablo; McCauley, Ross A.; Petersen, Gitte; Santos-Bay, Luisa; Wales, Nathan; Catchen, Julian M.; Machado, Daniel; Nowak, Michael D.; Suh, Alexander; Sinha, Neelima R.; Nielsen, Lene R.; Seberg, Ole; Gilbert, M. Thomas P.; Leebens-Mack, James H.; Rieseberg, Loren H.; Martin, Michael D.

In: Nature Communications, Vol. 13, 3729, 2022.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Cerca, J, Petersen, B, Lazaro-Guevara, JM, Rivera-Colón, A, Birkeland, S, Vizueta, J, Li, S, Li, Q, Loureiro, J, Kosawang, C, Díaz, PJ, Rivas-Torres, G, Fernández-Mazuecos, M, Vargas, P, McCauley, RA, Petersen, G, Santos-Bay, L, Wales, N, Catchen, JM, Machado, D, Nowak, MD, Suh, A, Sinha, NR, Nielsen, LR, Seberg, O, Gilbert, MTP, Leebens-Mack, JH, Rieseberg, LH & Martin, MD 2022, 'The genomic basis of the plant island syndrome in Darwin’s giant daisies', Nature Communications, vol. 13, 3729. https://doi.org/10.1038/s41467-022-31280-w

APA

Cerca, J., Petersen, B., Lazaro-Guevara, J. M., Rivera-Colón, A., Birkeland, S., Vizueta, J., Li, S., Li, Q., Loureiro, J., Kosawang, C., Díaz, P. J., Rivas-Torres, G., Fernández-Mazuecos, M., Vargas, P., McCauley, R. A., Petersen, G., Santos-Bay, L., Wales, N., Catchen, J. M., ... Martin, M. D. (2022). The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications, 13, [3729]. https://doi.org/10.1038/s41467-022-31280-w

Vancouver

Cerca J, Petersen B, Lazaro-Guevara JM, Rivera-Colón A, Birkeland S, Vizueta J et al. The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature Communications. 2022;13. 3729. https://doi.org/10.1038/s41467-022-31280-w

Author

Cerca, José ; Petersen, Bent ; Lazaro-Guevara, José Miguel ; Rivera-Colón, Angel ; Birkeland, Siri ; Vizueta, Joel ; Li, Siyu ; Li, Qionghou ; Loureiro, João ; Kosawang, Chatchai ; Díaz, Patricia Jaramillo ; Rivas-Torres, Gonzalo ; Fernández-Mazuecos, Mario ; Vargas, Pablo ; McCauley, Ross A. ; Petersen, Gitte ; Santos-Bay, Luisa ; Wales, Nathan ; Catchen, Julian M. ; Machado, Daniel ; Nowak, Michael D. ; Suh, Alexander ; Sinha, Neelima R. ; Nielsen, Lene R. ; Seberg, Ole ; Gilbert, M. Thomas P. ; Leebens-Mack, James H. ; Rieseberg, Loren H. ; Martin, Michael D. / The genomic basis of the plant island syndrome in Darwin’s giant daisies. In: Nature Communications. 2022 ; Vol. 13.

Bibtex

@article{dc65f041f8b74375b1bb2fc5fdd01abc,
title = "The genomic basis of the plant island syndrome in Darwin{\textquoteright}s giant daisies",
abstract = "The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the {\textquoteleft}plant island syndrome{\textquoteright}, 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, Gal{\'a}pagos-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{\textquoteright}s giant daisies.",
author = "Jos{\'e} Cerca and Bent Petersen and Lazaro-Guevara, {Jos{\'e} Miguel} and Angel Rivera-Col{\'o}n and Siri Birkeland and Joel Vizueta and Siyu Li and Qionghou Li and Jo{\~a}o Loureiro and Chatchai Kosawang and D{\'i}az, {Patricia Jaramillo} and Gonzalo Rivas-Torres and Mario Fern{\'a}ndez-Mazuecos and Pablo Vargas and McCauley, {Ross A.} and Gitte Petersen and Luisa Santos-Bay and Nathan Wales and Catchen, {Julian M.} and Daniel Machado and Nowak, {Michael D.} and Alexander Suh and Sinha, {Neelima R.} and Nielsen, {Lene R.} and Ole Seberg and Gilbert, {M. Thomas P.} and Leebens-Mack, {James H.} and Rieseberg, {Loren H.} and Martin, {Michael D.}",
note = "Funding Information: J.Ce. is grateful to Simen R. Sandve for fruitful discussion and Martin LaForest for sharing genome annotations. We thank Henning Adsersen for the botanical expertise and logistical support that enabled use of the University of Copenhagen botanical collections. Jennifer Mandel kindly shared the Asteraceae COS. The collection and photography of specimens, and the preparation of this manuscript, benefited enormously from the cooperative assistance of the personnel of the Charles Darwin Foundation Research Station, who made arrangements for collecting trips, arranged laboratory space, and offered encouragement and support throughout the project. Scalesia specimens were initially collected under Gal{\'a}pagos National Park research permit number PC-001/98 PNG and were further normalised via Ecuador Ministry of the Environment genetic permit number MAAE-DBI-CM-2021-0213. This publication is contribution number 2426 of the Charles Darwin Foundation for the Gal{\'a}pagos Islands. This work was supported by the Norwegian Research Council via project number 287327 awarded to M.D.M., and a travel grant (project number 287327) granted to J.Ce. and M.D.M. Publisher Copyright: {\textcopyright} 2022, The Author(s).",
year = "2022",
doi = "10.1038/s41467-022-31280-w",
language = "English",
volume = "13",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - The genomic basis of the plant island syndrome in Darwin’s giant daisies

AU - Cerca, José

AU - Petersen, Bent

AU - Lazaro-Guevara, José Miguel

AU - Rivera-Colón, Angel

AU - Birkeland, Siri

AU - Vizueta, Joel

AU - Li, Siyu

AU - Li, Qionghou

AU - Loureiro, João

AU - Kosawang, Chatchai

AU - Díaz, Patricia Jaramillo

AU - Rivas-Torres, Gonzalo

AU - Fernández-Mazuecos, Mario

AU - Vargas, Pablo

AU - McCauley, Ross A.

AU - Petersen, Gitte

AU - Santos-Bay, Luisa

AU - Wales, Nathan

AU - Catchen, Julian M.

AU - Machado, Daniel

AU - Nowak, Michael D.

AU - Suh, Alexander

AU - Sinha, Neelima R.

AU - Nielsen, Lene R.

AU - Seberg, Ole

AU - Gilbert, M. Thomas P.

AU - Leebens-Mack, James H.

AU - Rieseberg, Loren H.

AU - Martin, Michael D.

N1 - Funding Information: J.Ce. is grateful to Simen R. Sandve for fruitful discussion and Martin LaForest for sharing genome annotations. We thank Henning Adsersen for the botanical expertise and logistical support that enabled use of the University of Copenhagen botanical collections. Jennifer Mandel kindly shared the Asteraceae COS. The collection and photography of specimens, and the preparation of this manuscript, benefited enormously from the cooperative assistance of the personnel of the Charles Darwin Foundation Research Station, who made arrangements for collecting trips, arranged laboratory space, and offered encouragement and support throughout the project. Scalesia specimens were initially collected under Galápagos National Park research permit number PC-001/98 PNG and were further normalised via Ecuador Ministry of the Environment genetic permit number MAAE-DBI-CM-2021-0213. This publication is contribution number 2426 of the Charles Darwin Foundation for the Galápagos Islands. This work was supported by the Norwegian Research Council via project number 287327 awarded to M.D.M., and a travel grant (project number 287327) granted to J.Ce. and M.D.M. Publisher Copyright: © 2022, The Author(s).

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

U2 - 10.1038/s41467-022-31280-w

DO - 10.1038/s41467-022-31280-w

M3 - Journal article

C2 - 35764640

AN - SCOPUS:85132977043

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 3729

ER -

ID: 314394317