Gene recovery of two genome-filtration sequencing techniques when applied to the maize genome

The large size of the maize genome and the expectation that most of the genome is represented by repetitive elements is a challenge to standard genome sequencing techniques. Genome-filtration sequencing techniques may target gene-rich regions in the genome. Two such approaches, methylation filtration and high Cot selection, may provide rapid and cost-effective alternative to sequencing the maize genome. Approximately 450k sequence reads have been obtained from both methylation filtration (MF) and high Cot (HC) libraries, and these sequences have been clustered and assembled. An analysis was undertaken to examine whether MF and MC enrich for maize genes and target non-identical sequence space. Simple sequence repeat analysis and mapped marker coverage provide gauges to examine whether MF and HC sample identical sequence space. Marker hits also provide evidence that MF and HC enrich for unique genic portions of the genome. Finally, the identification of maize and other protein sequences in the MF and HC sequence sets can indicate the expected fraction and coverage of the maize gene space by MF and HC.