Easyquencing: A Repeated Sequences Filtration Strategy for NGS

Whole genome sequencing is often limited by the genome size that directly correlates to the costs of the sequencing which are still too high. With most part of the genome composed of repeated DNA it is desirable a strategy to reduce the repeated fraction. Such strategy would allow large scale SNP discovery, genotyping, local assembly in species with large genomes. We have developed a method for repetitive DNA subtraction and subsequent high throughput sequencing with Illumina technology suitable for both sequenced and unsequenced plant species. The method is based on C0t filtration and dsDNA cleavage with Duplex-specific nuclease. In order to evaluate the effect of the filtration strategy we analyzed Illumina MiSeq sequences obtained using libraries with logC₀t =1 and logC₀t=3 thresholds from Pisum sativum and Vitis vinifera gDNA. We report our results in comparison to sequences of unfiltered gDNA libraries from the same species.