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.

Abstract

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.

Citation

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. https://doi.org/10.1038/s41598-018-36304-4

• 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: Jan 29, 2021
• Journal: Scientific Reports
• Print ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 8
• Issue: 1
• Article Number: 17942
• DOI: https://doi.org/10.1038/s41598-018-36304-4
• Keywords: Comparative genomics; Genomics; Plant evolution; Plant reproduction; Transcriptomics
• Public URL: https://hull-repository.worktribe.com/output/3703587
• Publisher URL: https://www.nature.com/articles/s41598-018-36304-4
• Additional Information: Received: 15 March 2018; Accepted: 14 November 2018; First Online: 18 December 2018; : The authors declare no competing interests.