Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

Osborne, O. G.; Wood, D. P.; Dobreva, M. P.; Dunning, L. T.; Tucker, R.; Coates, S. E. R.; Pellicer, J.; Holmberg, J.; Algar, A. C.; Bocedi, G.; Gubry-Rangin, C.; Herrera-Alsina, L.; Juliandi, B.; Lancaster, L.; Touzet, P.; Travis, J. M.; Papadopulos, A.

doi:10.1101/2024.11.25.625183

bioRxiv · 10.1101/2024.11.25.625183

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

Osborne, O. G.·Wood, D. P.·Dobreva, M. P.·Dunning, L. T.·Tucker, R.·Coates, S. E. R.·Pellicer, J.·Holmberg, J.·Algar, A. C.·Bocedi, G.·Gubry-Rangin, C.·Herrera-Alsina, L.·Juliandi, B.·Lancaster, L.·Touzet, P.·Travis, J. M.·Papadopulos, A.

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Abstract

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

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Osborne, O. G., Wood, D. P., Dobreva, M. P., Dunning, L. T., Tucker, R., Coates, S. E. R., Pellicer, J., Holmberg, J., Algar, A. C., Bocedi, G., Gubry-Rangin, C., Herrera-Alsina, L., Juliandi, B., Lancaster, L., Touzet, P., Travis, J. M., Papadopulos, A.. 2024-11-25. Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species. https://doi.org/10.1101/2024.11.25.625183

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