Journal
APPLICATIONS IN PLANT SCIENCES
Volume 2, Issue 12, Pages -Publisher
WILEY
DOI: 10.3732/apps.1400062
Keywords
Amsinckiinae; Geneious; genome skimming; next-generation sequencing (NGS); Oreocarya; phylogenomics
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Funding
- Riverside County Community Foundation's Desert Legacy Grant
- California Native Plant Society
- American Society of Plant Taxonomists
- Southern California Botanists
- Northern California Botanists
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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.
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