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

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

doi:10.7554/eLife.36426

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

Journal Article · Tue Oct 16 00:00:00 EDT 2018 · eLife

DOI:https://doi.org/10.7554/eLife.36426· OSTI ID:1484210

^[1]; Ballerini, Evangeline S. ^[2]; Mandáková, Terezie ^[3]; Aköz, Gökçe ^[4]; Derieg, Nathan J. ^[2]; Schmutz, Jeremy ^[5]; Jenkins, Jerry ^[5]; Grimwood, Jane ^[5]; Shu, Shengqiang ^[6]; Hayes, Richard D. ^[6]; Hellsten, Uffe ^[6];

^[6]; Yan, Juying ^[6]; Mihaltcheva, Sirma ^[6]; Karafiátová, Miroslava ^[7]; Nizhynska, Viktoria ^[1]; Kramer, Elena M. ^[8]; Lysak, Martin A. ^[3]; Hodges, Scott A. ^[2];

^[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)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: 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 )

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1484210

Alternate ID(s):: OSTI ID: 1506371

Journal Information:: eLife, Vol. 7, Issue none; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 75 works

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The Aquilegia genome reveals a hybrid origin of core eudicots Aköz, Gökçe; Nordborg, Magnus Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1888-8	journal	November 2019
The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives Mandáková, Terezie; Zozomová-Lihová, Judita; Kudoh, Hiroshi Annals of Botany, Vol. 124, Issue 2 https://doi.org/10.1093/aob/mcz019	journal	March 2019
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia Piñeiro Fernández, Laura; Byers, Kelsey J. R. . P.; Cai, Jing Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01553	journal	November 2019
A phylogenomic analysis of the floral transcriptomes of sexually deceptive and rewarding European orchids, Ophrys and Gymnadenia Pineiro Fernandez, Laura; Byers, Kelsey J. R. P.; Cai, Jing Frontiers Research Foundation https://doi.org/10.5167/uzh-182304	text	January 2019
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia Piñeiro Fernández, Laura; . P., Byers, Kelsey J. R.; Cai, Jing Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.47323	text	January 2019
Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development Ballerini, Evangeline S.; Kramer, Elena M.; Hodges, Scott A. BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6002-9	journal	August 2019
Genome sequence of Malania oleifera , a tree with great value for nervonic acid production Xu, Chao-Qun; Liu, Hui; Zhou, Shan-Shan GigaScience, Vol. 8, Issue 2 https://doi.org/10.1093/gigascience/giy164	journal	January 2019
Fluorescence in situ hybridization in plants: recent developments and future applications Jiang, Jiming Chromosome Research, Vol. 27, Issue 3 https://doi.org/10.1007/s10577-019-09607-z	journal	March 2019
Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice Choi, Jae Young; Lye, Zoe N.; Groen, Simon C. Genome Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s13059-020-1938-2	journal	February 2020
Data from: The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history Filiault, Danièle L.; Ballerini, Evangeline S.; Mandakova, Terezie Dryad https://doi.org/10.5061/dryad.j4j12v0	dataset	January 2018
Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James) Sharma, Bharti; Batz, Timothy A.; Kaundal, Rakesh Genes, Vol. 10, Issue 10 https://doi.org/10.3390/genes10100734	journal	September 2019
Chromosome Painting Facilitates Anchoring Reference Genome Sequence to Chromosomes In Situ and Integrated Karyotyping in Banana (Musa Spp.) Šimoníková, Denisa; Němečková, Alžbeěta; Karafiátová, Miroslava Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01503	journal	November 2019