Abstract Detail


Carter, K.A. [1], Liston, A. [2], Alice, Lawrence [3], Bassil, N.V. [4], Bushakra, J.M. [4], Sutherland, B.L. [5], Hummer, Kim [4].

Target Capture Sequencing: application to phylogeny, biogeography, and divergence time for Rubus.

Rubus (Rosaceae), which includes a global distribution of 500 - 700 species of raspberries, blackberries, and wild relatives, is in need of subgeneric reassessment. Initial subgeneric definitions date back to the early 1900s. Previous phylogenetic analyses were based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequence data and other limited number of nuclear and chloroplast loci, including GBSSI-2, PEPC, trnL/F, rbcL, rpl20-rps12, and trnG-trnS. New molecular methods provide an opportunity for high throughput molecular analyses. We applied target capture sequencing to estimate the phylogenetic relationships within Rubus. Our objectives were to: estimate phylogeny for 93 globally diverse species using target capture of approximately 1,000 low copy nuclear genes and chloroplast sequences; calculate divergence times between major Rubus clades; and examine the biogeography of species diversification. We chose probe sequences from transcripts of 926 single copy black raspberry nuclear genes. In addition, we included probes for 247 single copy nuclear genes in common between apple, peach and strawberry sequences. Short-read sequencing was performed for 96 total libraries representing 12 subgenera and 3 economically important cultivars. This technique separated Rubus into eight groups with preliminary analysis differentiating certain members of subgenera Anoplobatus and Dalibardastrum into a unique clade relative to the remainder of the genus. Observed clades were similar to those previously seen in ITS-based trees, however, relationships among groups were different. Idaeobatus was polyphyletic, but the trees placed alternate Idaeobatus groups sister to the group containing subgenus Rubus. The phylogeny developed using targeted sequences provided additional resolution within groups, 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 subgeneric divisions of Rubus should be redefined. The most recent common ancestor was likely distributed in North America.  During the early Miocene, lineages could have migrated from North America to Asia and Europe over the Bering land bridge. Migrations to South America occurred during the formation of the Panamanian Isthmus in the mid- to late Miocene, and long-distance dispersal events may have allowed Rubus to spread from South America to Oceania. During the middle and late Miocene, the genus diversified greatly in Asia, Europe, South America and Oceania. Whole genome duplication events occurred producing species of higher ploidy. We will pursue studies to evaluate morphological variation in a phylogenetic context.

1 - Oregon State University
2 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, United States
3 - Biology, 1906 College Heights Blvd., Western Kentucky University, Bowling Green, KY, 42101, United States
4 - National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333, United States
5 - University of Arizona


Presentation Type: Poster This poster will be presented at 6:15 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PSY018
Abstract ID:691
Candidate for Awards:None

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