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

Abstract

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:
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); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )
OSTI Identifier:
1484210
Alternate Identifier(s):
OSTI ID: 1506371
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 7; Journal Issue: none; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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., 2018. 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. Tue . "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},
issn = {2050-084X},
number = none,
volume = 7,
place = {United States},
year = {2018},
month = {10}
}

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Cited by: 3 works
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Figures / Tables:

Figure 1 Figure 1: Distribution of Aquilegia species. There are ~70 species in the genus Aquilegia, broadly distributed across temperate regions of the Northern Hemisphere (grey). The 10 Aquilegia species sequenced here were chosen as representatives spanning this geographic distribution as well as the diversity in ecological habitat and pollinator-influenced floral morphologymore » of the genus. Semiaquilegia adoxoides, generally thought to be the sister taxon to Aquilegia (Fior et al., 2013), was also sequenced. A representative photo of each species is shown and is linked to its approximate distribution. DOI: https://doi.org/10.7554/eLife.36426.002 The following figure supplement is available for figure 1: Origin of species samples used for sequencing. DOI: https://doi.org/10.7554/eLife.36426.003« less

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Works referenced in this record:

Ab initio Gene Finding in Drosophila Genomic DNA
journal, April 2000

  • Salamov, Asaf A.; Solovyev, Victor V.
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