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Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

Cocker, Jonathan M.; Wright, Jonathan; Li, Jinhong; Swarbreck, David; Dyer, Sarah; Caccamo, Mario; Gilmartin, Philip M.


Jonathan M. Cocker

Jonathan Wright

Jinhong Li

David Swarbreck

Sarah Dyer

Mario Caccamo

Philip M. Gilmartin


Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species.


Cocker, J. M., Wright, J., Li, J., Swarbreck, D., Dyer, S., Caccamo, M., & Gilmartin, P. M. (2018). Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene. Scientific reports, 8(1), Article 17942.

Journal Article Type Article
Acceptance Date Nov 14, 2018
Online Publication Date Dec 18, 2018
Publication Date 2018-12
Deposit Date Jan 29, 2021
Publicly Available Date Oct 27, 2022
Journal Scientific Reports
Print ISSN 2045-2322
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 8
Issue 1
Article Number 17942
Keywords Comparative genomics; Genomics; Plant evolution; Plant reproduction; Transcriptomics
Public URL
Publisher URL
Additional Information Received: 15 March 2018; Accepted: 14 November 2018; First Online: 18 December 2018; : The authors declare no competing interests.


Published article (2.1 Mb)

Copyright Statement
© The Author(s) 2018. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit

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