2017 ASHS Annual Conference

Phylogenetic analyses in Rubus L. have been challenging due to polyploidy, hybridization, and apomixis within the genus. Wide morphological diversity occurs within and between species, contributing to challenges at lower and higher systematic levels. Phylogenetic inferences to date have been based on limited nuclear and chloroplast loci or have focused on one subgenus or section. To clarify complex infrageneric relationships in Rubus, a thorough sampling of each subgenus at multiple loci is needed. Target enrichment is an innovative phylogenomic approach that could provide clarity. The objective of our study was to use target enrichment to determine phylogenetic relationships within Rubus. Our target enrichment probe synthesis encompassed loci from the Rubus occidentalis L. genome and a comparison of the apple, peach and strawberry genomes. Specifically, we chose probe sequences from transcripts of 926 single copy R. occidentalis nuclear genes. In addition, we included probes for 247 single copy nuclear genes, as identified from the apple, peach and strawberry genome sequences. Illumina sequencing was performed for 96 enriched libraries, including representatives from each of 12 subgenera and five known hybrids or economically important cultivars. The final sequencing library contained a high proportion of the captured sequences, enabling high levels of sample multiplexing while retaining good depth of coverage at each locus. More than three species were sampled for each subgenus except for Comaropsis and the monotypic subgenus Chamaemorus. Representative samples from every continent on which Rubus is known were studied. Preliminary analysis differentiated certain members of subgenera Anoplobatus and Dalibardastrum into a unique clade relative to the remainder of the genus. Observed clades were similar to those seen in a previous nuclear ribosomal internal transcribed spacer (ITS) tree, however, relationships among clades were different. Idaeobatus was polyphyletic in the ITS and the target enrichment phylogeny, but the trees place alternate Idaeobatus clades sister to the clade containing subgenus Rubus. The target enrichment phylogeny provided additional resolution within clades, likely due to the increased number of loci. Orobatus was monophyletic and all species of subgenus Rubus except R. ursinus and R. caesius grouped together. Other subgenera were either para- or polyphyletic, suggesting that traditional subgeneric divisions of Rubus should be redefined. This robust dataset will produce further insights into the role of polyploidy and interspecific hybridization in the evolutionary history of Rubus.