Sequencing the Genome of Potentilla micrantha using the PacBio® RS High Resolution Genetic Analyzer Yields High Quality Sequence Contigs and Permits Comparisons with the Genome of the Woodland Strawberry, Fragaria vesca

Fruit development, a complex trait, has yet to be studied in a genome context. An international consortium sequenced the genome of the woodland strawberry (F. vesca) using short read sequencing (Shulaev et al 2011). The genome sequence consists of 247 scaffolds containing 96% of the scaffolded sequence, and 34,809 gene predictions. To date, no Fragaria mutants lacking fruit-bearing structures have been characterised. Fragaria is closely related to Potentilla, a genus of flowering plants where many species, such as P. micrantha, lack fleshy ‘fruits’ or berries. Despite this, P. micrantha is remarkably similar to F. vesca. Comparative genomics between these plants will yield significant information regarding the genetic mechanisms controlling fruit development. Exploiting the latest high throughput sequencing methodologies developed by Pacific Biosciences, we sequenced the P. micarantha genome using continuous long reads from a 10kb genomic DNA library and SMRT sequencing technology. We have produced a draft genome sequence, spanning the majority of the predicted sequence length, demonstrating that it is a highly homozygous genome, relatively devoid of repetitive DNA, with an estimated size of 240 Mb. A comparison of sequence data produced using the Illumina HiSeq2000 and the PacBio RS platform demonstrated that PacBio sequencing produced a significantly longer N50 contig size and permitted a more complete genome assembly than could be achieved using data derived from short-read sequencing alone. The resultant draft genome sequence will be used for more extensive comparative studies with the F. vesca genome to elucidate the genetic basis of fruit development.