Data from: Geneious! Simplified genome skimming methods for phylogenetic systematic studies: a case study in Oreocarya (Boraginaceae)

Premise of the study: 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. Discussion:
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.