Insights from the genomes of four diploid Camelina spp.

Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plants genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with three unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativas formation, we sequenced and assembled chromosome level draft genomes for four diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativas sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativas sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativas sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativas genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.