Abstract Detail

Phylogenomics

Ripma, Lee [1], Simpson, Michael [2].

From Pectinate to Divaricate: Phylogenetic Systematics of Oreocarya (Boraginaceae) Using Shallow Genome Skimming.

Next-generation sequencing (NGS) is rapidly transforming the molecular systematic study of non-model plant taxa. One such taxon is Oreocarya, a genus of 71 taxa of the Boraginaceae, subtribe Cryptanthinae. The approximately nine genera of Cryptanthinae, including Oreocarya, have been the subject of much taxonomic study over the last 100 years. Taxa appear morphologically similar to one another when flowers and vegetative characters are examined; consequently taxonomists have focused primarily on the variable characteristics of the fruits (“nutlets”) to differentiate genera and species. More recently, systematists have gathered DNA sequence data using a standard method of PCR amplification and Sanger sequencing of a few gene markers. This has proven useful in recovering the major clades of subtribe Cryptanthinae, but lower level taxonomic resolution has been lacking. To test the utility of using NGS shallow genome skimming for taxonomic studies within Cryptanthinae, 100-bp single-end Illumina reads were generated for 21 taxa of Oreocarya and outgroups in half of an Illumina HiSeq lane, resulting in 1.7-9 million reads per taxon. Reference-guided assembly was used to recover sequences of the plastome and nrDNA cistron. De novo assemblies were searched for orthologous markers shared among sample taxa, which were used to infer phylogenies using Maximum Likelihood and Bayesian methods. Our study suggests that shallow genome skimming provides much improved data for phylogenetic resolution at lower level taxonomic levels and is a viable way to approach systematic studies of the Cryptanthinae complex.

Broader Impacts:

Related Links:
Oreocarya Taxonomy and Images at San Diego State University

1 - San Diego State University, Department of Biology, San Diego, CA, 92182-4416, USA
2 - San Diego State University, Department of Biology, San Diego State University, San Diego, CA, 92182-4416, USA

Keywords:
Phylogenetics
Oreocarya
Boraginaceae
next generation sequencing.

Presentation Type: Oral Paper:Papers for Topics
Session: 36
Location: Magnolia/Riverside Hilton
Date: Tuesday, July 30th, 2013
Time: 5:00 PM
Number: 36014
Abstract ID:838
Candidate for Awards:Margaret Menzel Award