Genomic Survey Sequences and the Structure of the Rubus chamaemorus L. and Rubus arcticus L. Genomes As Determined By Double Digest Restriction Associated Digest-(ddRAD) Tags

Rubus idaeus L. and Rubus chamaemorus L. are two economically important berry species in Northern Europe and Scandinavia and both produce aggregate fruit of numerous drupelets around a central core, yet they differ in many other traits. Moreover R. chamaemorus, and the related species R. arcticus, grow in subartic circumpolar environments where little domestication has taken place, whereas R. ideaus is commonly cultivated in a range of other climates and has been bred for specific horticultural traits. R. ideaus is also diploid, and contains seven linkage groups, and has a genome size of around 275 Mb. In comparison R. chamaemorus is octoploid and R. arcticus tetraploid, though little else is known about genome structure and organization. We are now clarifying the genomes of the later two species by reduced representation sequencing using a streamlined ddRAD tag protocol optimized for the Ion Torrent sequencing platform. Our strategy uses restriction enzymes that infrequently cut the genome so as to maximize the depth of sequencing at specifically tagged loci, an attribute that is needed to accurately call variants between sister chromatids in polyploids. Our sequencing effort compares R. ideaus, R. articus and several released R. chamaemorus selections, which are confirmed as stable and high yielding, and includes an R. chamaemorus F₁ series. ddRAD tag sequences that represent several megabases of each genome have been generated. From this we hope to determine the polyploidization mode and the degree in which comparative genomics can be applied across Rubus and other Roseaceous genomes.