Chromosome-level genome assembly for the angiospermSilene conica

Author:

Fields Peter D.ORCID,Weber Melody M.,Waneka GusORCID,Broz Amanda K.ORCID,Sloan Daniel B.ORCID

Abstract

AbstractThe angiosperm genusSilenehas been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome ofSilene conicabased on PacBio HiFi, Hi-C and Bionano technologies. The assembly produced 10 scaffolds (one per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations thatS. conicaand its relatives have a reduced base chromosome number relative to the genus’s ancestral state of 12.Silene conicahas an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies inSilene, including comparative analyses with related species that recently evolved sex chromosomes.SignificanceWhole-genome sequences have been largely lacking for species in the genusSileneeven though these flowering plants have been used for studying ecology, evolution, and genetics for over a century. Here, we address this gap by providing a high-quality nuclear genome assembly forS. conica, a species known to have greatly accelerated rates of sequence and structural divergence in its mitochondrial and plastid genomes. This resource will be valuable in understanding the coevolutionary interactions between nuclear and cytoplasmic genomes and in comparative analyses across this highly diverse genus.

Publisher

Cold Spring Harbor Laboratory

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