title: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: A case study in Oreocarya (Boraginaceae).
abstract: OBJECTIVE
  As systematists grapple with how to best harness the power of next-generation sequencing (NGS), a deluge of review papers, methods, and analytical tools make choosing the right method difficult. Oreocarya (Boraginaceae), a genus of 63 species, is a good example of a group lacking both species-level resolution and genomic resources. The use of Geneious removes bioinformatic barriers and makes NGS genome skimming accessible to even the least tech-savvy systematists. •
  
  
  METHODS
  A combination of de novo and reference-guided assemblies was used to process 100-bp single-end Illumina HiSeq 2000 reads. A subset of 25 taxa was used to test the suitability of genome skimming for future systematic studies in recalcitrant lineages like Oreocarya. •
  
  
  RESULTS
  The nuclear ribosomal cistron, the plastome, and 12 mitochondrial genes were recovered from all 25 taxa. All data processing and phylogenomic analyses were performed in Geneious. We report possible future multiplexing levels and published low-copy nuclear genes represented within de novo contigs. •
  
  
  CONCLUSIONS
  Genome skimming represents a much-improved primary data collection over PCR+Sanger sequencing when chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and mitochondrial DNA (mtDNA) are the target sequences. This study details methods that plant systematists can employ to study their own taxa of interest.
authors.affiliation: Department of Biology, San Diego State University, San Diego, California 92182-4614 USA.
authors.forename: Lee A
authors.initials: LA
authors.lastname: Ripma
authors.affiliation: Department of Biology, San Diego State University, San Diego, California 92182-4614 USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Simpson
authors.affiliation: Rancho Santa Ana Botanic Garden, 1500 N. College Avenue, Claremont, California 92117 USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Hasenstab-Lehman
keywords: Amsinckiinae; Geneious; Oreocarya; genome skimming; next-generation sequencing (NGS); phylogenomics