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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: Target capture sequencing unravels Rubus evolution

Author
item CARTER, KATIE - OREGON STATE UNIVERSITY
item LISTON, AARON - OREGON STATE UNIVERSITY
item Bassil, Nahla
item ALICE, LARENCE - WESTERN KENTUCKY UNIVERSITY
item Bushakra, Jill
item SUTHERLAND, BRITTANY - UNIVERSITY OF ARIZONA
item MOCKLER, TODD - DANFORTH PLANT SCIENCE CENTER
item BRYANT, DOUGLAS - DANFORTH PLANT SCIENCE CENTER
item Hummer, Kim

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/15/2019
Publication Date: 12/20/2019
Citation: Carter, K.A., Liston, A., Bassil, N.V., Alice, L.A., Bushakra, J., Sutherland, B.L., Mockler, T.C., Bryant, D.W., Hummer, K.E. 2019. Target capture sequencing unravels Rubus evolution. Frontiers in Plant Science. 10:1615. https://doi.org/10.3389/fpls.2019.01615.
DOI: https://doi.org/10.3389/fpls.2019.01615

Interpretive Summary: Background: The canberries comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of berry species challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species, and 3 cultivars, using chloroplast DNA sequences and target capture of approximately 1,000 nuclear genes; estimate divergence times between major family groups; and examine the historical biogeography of species diversification. Results: Target capture sequencing is a new technique that was applied. This technique worked more precisely than methods that looked only at 1 or a few genes. This technique identified eight major groups within the canberry family. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor was most likely distributed in North America rather than China as had been originally thought. Beginning during the Miocene (about 20 Ma) multiple distribution events occurred from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. These canberry species diversified greatly in Asia during the Miocene. Conclusions: Canberry species names do not reflect family relationships and revision of the species groupings is warranted. Target capture sequencing confirmed that most of the presently named groups were not consistent. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the present day berry species may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further berry research.

Technical Abstract: Background: Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species, and 3 cultivars, using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Results: Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while several other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Beginning during the Miocene (about 20 Ma) multiple distribution events occurred from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Conclusions: Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research.