Growing the Next Generation in Plant Genomics
Straub, Shannon , Hansen, Kimberly , Fishbein, Mark , Cronn, Richard , Liston, Aaron .
Skimming the cream of the milkweed genome for next-generation plant systematics.
The advent of next-generation sequencing combined with multiplex sequencing approaches is changing the way we design molecular phylogenetics studies by alleviating the systematist's dilemma of choosing between more taxa and more characters. Using both deep sequencing in an exemplar species and shallow sequencing (genome skimming) of related species, a great deal of information may be obtained about the three genomes of plants: nuclear, plastid, and mitochondrial. We have applied this approach in 105 species of North American Asclepias (Apocynaceae), an example of a recent, rapid evolutionary radiation whose phylogenetic relationships have been difficult to elucidate using traditional molecular systematics methods. In general, phylogenetic analysis of data from whole plastid genomes and the nuclear genome yielded a well-resolved and highly supported phylogeny of Asclepias; however limited variability in mitochondrial genome sequences has hampered their use for phylogeny reconstruction. Cases of cyto-nuclear incongruence of relationships indicate a more complex history of several species. Future targeted sequencing of single-copy nuclear genes will reveal more of the evolutionary history of this genus as we move from analyzing collections of gene trees toward a species tree for Asclepias. These results highlight the utility and promise of next-generation sequencing for phylogenomics and genome exploration in plants by the next generation of plant systematists.
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1 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
2 - Oklahoma State University, Dept Of Botany, 301 Physical Science, Stillwater, OK, 74078, USA
3 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
next generation sequencing
Presentation Type: Symposium or Colloquium Presentation
Location: Franklin C and D/Hyatt
Date: Monday, July 9th, 2012
Time: 2:30 PM