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:
-
[1];
[6];
[1]
- Austrian Academy of Sciences, Vienna (Austria)
- Univ. of California, Santa Barbara, CA (United States)
- Masaryk Univ., Brno (Czech Republic)
- Austrian Academy of Sciences, Vienna (Austria); Vienna Graduate School of Population Genetics, Vienna (Austria)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute of Biotechnology, Huntsville, AL (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc (Czech Republic)
- Harvard Univ., Cambridge, MA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); 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:
- 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. https://doi.org/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. https://doi.org/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 = {Tue Oct 16 00:00:00 EDT 2018},
month = {Tue Oct 16 00:00:00 EDT 2018}
}
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Figures / Tables:
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 »
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A phylogenomic analysis of the floral transcriptomes of sexually deceptive and rewarding European orchids, Ophrys and Gymnadenia
text, January 2019
- Pineiro Fernandez, Laura; Byers, Kelsey J. R. P.; Cai, Jing
- Frontiers Research Foundation
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia
text, January 2019
- Piñeiro Fernández, Laura; . P., Byers, Kelsey J. R.; Cai, Jing
- Apollo - University of Cambridge Repository
Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development
journal, August 2019
- Ballerini, Evangeline S.; Kramer, Elena M.; Hodges, Scott A.
- BMC Genomics, Vol. 20, Issue 1
Genome sequence of Malania oleifera , a tree with great value for nervonic acid production
journal, January 2019
- Xu, Chao-Qun; Liu, Hui; Zhou, Shan-Shan
- GigaScience, Vol. 8, Issue 2
Fluorescence in situ hybridization in plants: recent developments and future applications
journal, March 2019
- Jiang, Jiming
- Chromosome Research, Vol. 27, Issue 3
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
journal, February 2020
- Choi, Jae Young; Lye, Zoe N.; Groen, Simon C.
- Genome Biology, Vol. 21, Issue 1
Data from: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history
dataset, January 2018
- Filiault, Danièle L.; Ballerini, Evangeline S.; Mandakova, Terezie
- Dryad
Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James)
journal, September 2019
- Sharma, Bharti; Batz, Timothy A.; Kaundal, Rakesh
- Genes, Vol. 10, Issue 10
Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.)
journal, November 2019
- Šimoníková, Denisa; Němečková, Alžbeěta; Karafiátová, Miroslava
- Frontiers in Plant Science, Vol. 10
Data from: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history
dataset, January 2018
- Filiault, Danièle L.; Ballerini, Evangeline S.; Mandakova, Terezie
- Dryad
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.