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

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

doi:10.1038/s41598-018-36304-4

Jonathan M Cocker, Jonathan M Cocker + Show 13 more

Open Access

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

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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.

Highlights

Floral heteromorphy in Primula has been studied for over 150 years
Our phylogenetic studies revealed an estimated divergence of 51.7 MYA for GLO-GLOT27, which suggests a single origin for heterostyly in the Primulaceae, and led us to predict that the S locus structure might be shared amongst Primula species
These previous findings raised new questions that we explore in the current manuscript: we address whether the hemizygosity of the S locus and its constituent genes is conserved in different Primula species; given this, we examine genomic features in the non-recombining S locus to determine how unique the region is compared to the wider genome; and, we explore genome-wide differential gene expression, using the comprehensive geneset defined in our P. vulgaris genome assembly, to identify potential direct and indirect downstream targets of this regulatory locus

Summary

Introduction

Floral heteromorphy in Primula has been studied for over 150 years. Charles Darwin first recognized the importance of this breeding system for promoting cross-pollination[1,2]; observations on its existence date back even further[3]. In heterostylous Primula species, plants produce one of two forms of flower, pin or thrum, with anthers and stigma in reciprocal positions (Fig. 1) This arrangement physically promotes insect-mediated outcrossing between the two floral morphs. Darwin investigated the effects of cross and self-fertilization in numerous species[7]; he observed reduced seed set from within-morph crosses of Primula, and proceeded to define heterostyly as a mechanism to ensure outcrossing, and avoid the potential ill-effects of inbreeding on height, vigour and fertility[2] This remarkable floral innovation is a striking example of convergent evolution, having evolved independently on at least 23 occasions, in 28 angiosperm families[8,9]. Our phylogenetic studies revealed an estimated divergence of 51.7 MYA for GLO-GLOT27, which suggests a single origin for heterostyly in the Primulaceae, and led us to predict that the S locus structure might be shared amongst Primula species

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