Abstract Detail

Phylogenomics

Wickett, Norman [1], Johnson, Matthew [2], Botigue, Laura [3], Devault, Alison [4], Dodsworth, Stephen [3], Forest, Felix [5], Kim, Jan [3], Leebens-Mack, Jim [6], Soltis, Douglas [7], Soltis, Pamela S. [8], Baker, William J. [9], Pokorny, Lisa [9].

Designing and testing a kit to enrich phylogenetically informative exons for all angiosperms.

Sequencing of target enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogenetic reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole genome duplication events, especially in the angiosperms. We used alignments of over 600 angiosperms for 353 putatively single-copy protein coding genes to design targeted sequencing probes that would be useful for phylogenetics in any flowering plant. To select between 5 and 15 sequences for each locus to use for probe design, we employed a k-medoids clustering approach which more efficiently represented angiosperm sequence diversity compared to using only published genomes. To test our approximately 80,000 probe sequences, we captured sequences from 42 species representing nearly all orders of angiosperms. We recovered exon sequence for 100 or more loci in all species, which was not affected by similarity to the taxa selected as medoids in probe design. These results suggest the probe design is effective in any group of flowering plants and would be useful for studies in phylogenetics of lineages at any taxonomic level.

1 - Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States
2 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States
3 - Royal Botanic Gardens, Kew, The Jodrell Laboratory, Richmond, UK
4 - Arbor Biosciences, 5840 Interface Dr, Suite 101, Ann Arbor, MI, 48103, USA
5 - Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3DS, UK
6 - University Of Georgia, Plant Biology, 2101 Miller Plant Sciences, Athens, GA, 30602, United States
7 - University of Florida, Biology, Gainesville, FL
8 - University of Florida, Florida Museum of Natural History, 1659 Museum Road, Gainesville, FL, 32611, US
9 - Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK

Keywords:
HybSeq
HybPiper
Sequence capture
Machine Learning
single-copy nuclear genes.

Presentation Type: Oral Paper
Session: 36, Phylogenomics III
Location: 107/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 9:00 AM
Number: 36005
Abstract ID:809
Candidate for Awards:None