S19 - Session O1 - Pan genome of strawberry varieties in Japan

Authors: Isobe Sachiko *, Kenta Shirasawa, Hideki Hirakawa, Megumi Hamano, Katsutoshi Ryu, Takeshi Kurokura

Strawberry ( Fragaria x ananassa ) is an octoploid species with an estimated genome size of about 800 Mb. The whole genomes of seven strawberry cultivars, Donner, Hokowase, Aiberry, Toyonoka, Sachinoka, Reikou and Nyoho, was sequenced in order to clarify the differences in genome structure among the varieties bred in Japan. Genome sequences were obtained using PacBio Sequel II with each one SMRT cell for a variety. Total length of generated HiFi reads ranged from 23.1 Gb to 31.4 Gb, representing 29-37x of the strawberry genome. De novo assembly was performed by using Hifiasm. Total lengths of assembled primary contigs ranged from 820 to 929 Mb with N50 lengths of 16.6 -26.0 Mb. Meanwhile, sum lengths of primary and haplotig contigs ranged from 1,334.3 (Nyoho) n 1,520.2 Mb (Aiberry). Primary contig sequences represented haploid genome, while haplotig sequences were created for heterozygous regions on the genome. The homozygous regions were not included in haplotig sequences, therefore the total length of primary contigs and haplotigs become shorter when the genome was highly homozygous. Ratios of haplotig contigs against the total length of primary and haplotig contigs ranged from 37% (Hokowase) to 46% (Aiberry). In general, varieties with newer registered years tended to show lower heterozygosity, because same strains have repeatedly used as parents. However, Aiberry showed higher heterozygosity than its ancestors, Hokowase and Reikou.