ISSRseq: An extensible method for reduced representation sequencing

The capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of biology, including crop breeding, pathology, forensics, forestry, ecology, evolution and conservation. However, the wet-laboratory expertise bioinformatics training required conduct genome-scale variant discovery remain limiting factors for investigators with limited resources. Here we present ISSRseq, a PCR-based method reduced representation genomic variation using simple sequence repeats as priming sites inter repeat (ISSR) regions. Briefly, ISSR regions are amplified primers, pooled, used construct sequencing libraries commercially available kit, sequenced on Illumina platform. We also flexible bioinformatic pipeline that assembles loci, calls hard filters variants, outputs matrices common formats, conducts population analyses R. Using three angiosperm species case studies, demonstrate ISSRseq highly repeatable, necessitates only skills commonplace instrumentation, terms number primers used, can genomic-scale par existing RRS methods which require more complex procedures. represents straightforward approach SNP genotyping any organism, predict this will be particularly useful those studying genomics phylogeography non-model organisms. Furthermore, ease relative other should prove lacking advanced or bioinformatics.