Where is plant systematics headed in the next ten years?
Soltis, Douglas .
The potential of genomics in plant systematics.
Next-generation sequencing (NGS) has completely revolutionized evolutionary biology, making it possible to investigate in depth the many non-genetic model systems that serve as great evolutionary models. We and others have used diverse methods of next-generation sequencing to address a suite of evolutionary questions. 454 sequencing has been used to obtain the complete genome sequence of Amborella; this genome will serve as an evolutionary reference genome, given its position as sister to all other living angiosperms. Illumina sequencing has facilitated an assessment of the transcriptomes of 1000 greenplants. This wealth of data has made it possible to compile a large data set of nuclear gene sequences, permitting new insights into phylogeny and ancient genome-wide duplication events. These Illumina runs have also yielded nearly complete plastid genomes, as well as a wealth of mtDNA genes, further facilitating detailed analyses of phylogeny. Phylogeographic and population alanalyses based on the complete (or nearly so) plastid genome will soon be routine. NGS is also providing unprecedented insights into polyploidy. In addition to elucidating ancient events, NGS approaches have also enabled us to obtain genome-scale data for Tragopogon (Asteraceae), an evolutionary model for the study of recent and repeated all opolyploidy. Although an evolutionary model, until now Tragopogon has been under-resourced as a genetic model. Using 454 and Illumina sequencing of the parental diploid species of T. miscellus,we identified thousands of single nucleotide polymorphisms that differ between the two parental nuclear genomes present in this allotetraploid. We used Sequenom MassARRAY iPLEX genotyping to examine patterns of presence/absence in numerous genes and plants from natural populations. We are employing 454 and Illumina sequencing to obtain a first-draft, low-coverage nuclear genome for Tragopogon, at relatively low cost. We have used NGS to develop micosatellite markers for population genetics and for probe development in FISH (fluorescent in situ hybridization) cytogenetics. The evolutionary applications of NGS approaches seem limited largely by one's imagination and budget.
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1 - University of Florida, Biology and Florida Museum of Natural History, Gainesville, FL, 32605, USA
next generation sequencing
Presentation Type: Symposium or Colloquium Presentation
Location: Franklin A/Hyatt
Date: Tuesday, July 10th, 2012
Time: 3:45 PM