De novo Assembly of the Diploid Strawberry Fragaria Iinumae Genome

Fragaria iinumae Makino, a member of the family Rosaceae, is a diploid (2n=2x=14) strawberry species with small genome size of about 240 MB. It is recognized as an ancestor of the octoploid strawberry species, including the cultivated strawberry, Fragaria × ananassa Duchesne ex Rozier. In order to facilitate genomic studies of the cultivated strawberry, we assembled the genome of F. iinumae accession F1D by integrating different and complementary data types including Illumina paired-end and mate pair reads, PacBio reads, optical mapping data, and a high resolution genetic linkage map. An initial de novo assembly was done by ALLPATHS-LG using short sequencing reads, followed by further scaffolding and gap-closing incorporating PacBio reads using PBJelly. Then optical data were generated using BioNano technology by the Bioinformatics Center at Kansas State University and were used to super-scaffold 54% of the draft assembly, increasing the scaffold N50 from 0.6Mb to 1.4 Mb. In parallel, a genetic map consisting of 3,280 Axiom IStraw90® array SNP markers and 893 GBS markers was constructed from a population of 104 F2 progeny derived from F1D. Furthermore, 22 of these individuals were genotyped by whole genome re-sequencing on the Illumina platform, thus contributing an additional 23,203 markers for the genetic map. Finally, the resulting ultra-high density genetic map was used by ALLMAPs to create seven pseudo-molecules, consisting of 1201 anchored scaffolds and representing 97% of the genome assembly. The release of the Fragaria iinumae reference genome provides a platform for detailed analysis of strawberry genome structure, variation, and evolution.