Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study in Oreocarya (Boraginaceae)

Genome Skimming

Ripma, Simpson and Hasenstab-Lehman recently published their research which involved developing methods for processing genome skimming data in the user-friendly program Geneious, and used genome skimming for systematic studies in Oreocarya (Boraginaceae).  The genome skimming method was selected for this study due to a lack of baseline genomic resources from which to design nuclear exon probes and the relative low-cost of gDNA library preparation which was performed using the NEXTflex™ DNA-Seq Kit. The NGS genome skimming method (initially developed by Straub et al., 2012) was used to assemble the high-copy fraction of total genomic DNA (gDNA) into the nuclear ribosomal cistron (nrDNA), plastome (cpDNA), and individual mitochondrial genes (mtDNA) without genome reduction during library preparation. With shallow sequencing of the nuclear DNA (nDNA), deeper sequencing for the high-copy fraction of gDNA is achieved. Additionally, these data generate baseline information from the nDNA to identify known single-copy and low-copy nuclear genes (LCNG) that can be used for future targeted sequencing studies. 

Ripma, L. A., Simpson, M. G. and Hasenstab-Lehman, K. (2014) Geneious! Simplified Genome Skimming Methods for Phylogenetic Systematic Studies: A Case Study in Oreocarya (Boraginaceae). Applications in Plant Sciences 2(12):1400062. doi: http://dx.doi.org/10.3732/apps.1400062.


 

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