Abstract Detail



Systematics

Carter, Katherine A. [1], Alice, Lawrence A. [2], LISTON, AARON [3], Mockler, Todd C. [4], Bryant, Douglas W.  [5], Bushakra, Jill [6], Bassil, Nahla [6], Hummer, Kim E. [7].

Increased Phylogenetic Resolution Using Target Capture of Nuclear Loci in Rubus.

Phylogenetic analyses in Rubus L. have been challenging due to polyploidy, hybridization, and apomixis. Wide morphological diversity occurs within and between species, contributing to challenges at lower and higher taxonomic 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 capture is an innovative phylogenomic approach that could provide clarity. The objective of our study was to use target capture to determine phylogenetic relationships within Rubus. Our target capture probe synthesis encompassed 926 single copy loci from the Rubus occidentalis L. genome and 247 loci from a comparison of the apple, peach and strawberry genomes. Illumina sequencing was performed for 96 enriched libraries, including representatives from each of 12 subgenera and five known hybrids or economically important cultivars. 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. Phylogenies were created from the assembled sequence data using ASTRAL-II and SVDQuartets. The resulting trees consistently showed eight different clades. This preliminary analysis indicates certain members of subgenera Anoplobatus, Dalibarda and Chamaemorus (1, 2) are sister to the remainder of the genus. Idaeobatus was polyphyletic with members occurring in five out of eight clades. The phylogenetic network identifies a number of polyploid taxa as potential hybrids, indicated by their intermediate position between two major clades. Known hybrids ‘Marion’, ‘Logan’ and ‘Boysen’ are seen between the raspberry (7) and blackberry (8) clades. Future work will include analysis of chloroplast genomes and mapping of ancestral traits to assess convergent evolution.


1 - Oregon State University, Horticulture, 4017 Agriculture and Life Sciences Building, Corvallis, OR, 97331, USA
2 - Western Kentucky University, Dept. of Biology, 1906 College Heights Blvd., Bowling Green, KY, 42101, USA
3 - Oregon State University, Department of Botany and Plant Pathology, Cordley Hall, Corvallis, OR, 97331, USA
4 - Danforth Center , 975 N. Warson Rd. , St. Louis, MO, 63132, USA
5 - Donald Danforth Plant Science Center, 975 North Warson Road , St. Louis, MO, 63132, USA
6 - USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd, Corvallis, OR, 97333, USA
7 - National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333, United States

Keywords:
Rubus
Targeted Sequence Capture
Phylogenomics
Rosaceae.

Presentation Type: Poster
Number: PSY016
Abstract ID:616
Candidate for Awards:None


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