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Title: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea ‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
Authors:
ORCiD logo [1] ;  [2] ;  [3] ;  [4] ;  [2] ;  [5] ;  [5] ;  [5] ;  [6] ;  [6] ;  [6] ; ORCiD logo [6] ;  [6] ;  [6] ;  [7] ;  [1] ;  [8] ;  [3] ;  [2] ; ORCiD logo [1]
  1. Austrian Academy of Sciences, Vienna (Austria)
  2. Univ. of California, Santa Barbara, CA (United States)
  3. Masaryk Univ., Brno (Czech Republic)
  4. Austrian Academy of Sciences, Vienna (Austria); Vienna Graduate School of Population Genetics, Vienna (Austria)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc (Czech Republic)
  8. Harvard Univ., Cambridge, MA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 7; Journal Issue: none; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1484210

Filiault, Danièle L., Ballerini, Evangeline S., Mandáková, Terezie, Aköz, Gökçe, Derieg, Nathan J., Schmutz, Jeremy, Jenkins, Jerry, Grimwood, Jane, Shu, Shengqiang, Hayes, Richard D., Hellsten, Uffe, Barry, Kerrie, Yan, Juying, Mihaltcheva, Sirma, Karafiátová, Miroslava, Nizhynska, Viktoria, Kramer, Elena M., Lysak, Martin A., Hodges, Scott A., and Nordborg, Magnus. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. United States: N. p., Web. doi:10.7554/eLife.36426.
Filiault, Danièle L., Ballerini, Evangeline S., Mandáková, Terezie, Aköz, Gökçe, Derieg, Nathan J., Schmutz, Jeremy, Jenkins, Jerry, Grimwood, Jane, Shu, Shengqiang, Hayes, Richard D., Hellsten, Uffe, Barry, Kerrie, Yan, Juying, Mihaltcheva, Sirma, Karafiátová, Miroslava, Nizhynska, Viktoria, Kramer, Elena M., Lysak, Martin A., Hodges, Scott A., & Nordborg, Magnus. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. United States. doi:10.7554/eLife.36426.
Filiault, Danièle L., Ballerini, Evangeline S., Mandáková, Terezie, Aköz, Gökçe, Derieg, Nathan J., Schmutz, Jeremy, Jenkins, Jerry, Grimwood, Jane, Shu, Shengqiang, Hayes, Richard D., Hellsten, Uffe, Barry, Kerrie, Yan, Juying, Mihaltcheva, Sirma, Karafiátová, Miroslava, Nizhynska, Viktoria, Kramer, Elena M., Lysak, Martin A., Hodges, Scott A., and Nordborg, Magnus. 2018. "The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history". United States. doi:10.7554/eLife.36426. https://www.osti.gov/servlets/purl/1484210.
@article{osti_1484210,
title = {The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history},
author = {Filiault, Danièle L. and Ballerini, Evangeline S. and Mandáková, Terezie and Aköz, Gökçe and Derieg, Nathan J. and Schmutz, Jeremy and Jenkins, Jerry and Grimwood, Jane and Shu, Shengqiang and Hayes, Richard D. and Hellsten, Uffe and Barry, Kerrie and Yan, Juying and Mihaltcheva, Sirma and Karafiátová, Miroslava and Nizhynska, Viktoria and Kramer, Elena M. and Lysak, Martin A. and Hodges, Scott A. and Nordborg, Magnus},
abstractNote = {The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea ‘Goldsmith’, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome – a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.},
doi = {10.7554/eLife.36426},
journal = {eLife},
number = none,
volume = 7,
place = {United States},
year = {2018},
month = {10}
}

Works referenced in this record:

Ab initio Gene Finding in Drosophila Genomic DNA
journal, April 2000
  • Salamov, Asaf A.; Solovyev, Victor V.
  • Genome Research, Vol. 10, Issue 4, p. 516-522
  • DOI: 10.1101/gr.10.4.516