De novo Whole Genome Assembly in Allo-Octoploid Strawberry

Strawberry (Fragaria × ananassa) is an allo-octoploid (2n=8X=56) and allogomous species. The whole genome sequence of strawberry was published by Hirakawa et al. (2014). Although the data has contributed genetic analysis in strawberry, the assembled sequences consisted of large number of sequences with short N50 length, suggested the necessary of further improvement. Therefore we performed de novo whole genome assembly again by using DenovoMAGIC which was developed in NRGene.　A Japanese variety, ‘Reikou’, was used for construction of paired end (PE), mate pair (MP) and 10X genomics libraries. Illumina reads with 250 nt (PE) and 160 nt (MP and 10X) were obtained by HiSeq platforms, and assembled by DenovoMAGIC3.0. The total length of the assembled sequences was 1,406 Mb, consisted of 32,715 sequences and N50 of 3.9 Mb. Meanwhile, a high-density genetic linkage map was constructed with an S₁ mapping population of ‘Reikou’ by mapping SNPs on the IStraw 90K Axiom® Array and previously published SSR markers. The ‘Reikou’ linkage map was consisted of 11,608 loci spanning 2,827.4 cM of 31 linkage groups. A total of 62 (31 × 2 haplotypes) pseudomolecules were developed based on the linkage map in a total length of 1,125 Mb. By comparison with the linkage map, 40 mis-assembly was found in the scaffolds. The mapping result of the pseudomolecules on the genome of F. vesca, a possible diploid ancestor of strawberry, clearly indicated the different structure of the four homoeologous genomes in strawberry. This is the first report on the pseudomolecules developed in strawberry, which is expected to accelerate genomics, genetics and molecular breeding for strawberry.