Pan genome of strawberry cultivars in Japan

S. Isobe, K. Shirasawa, H. Hirakawa, M. Hamano, K. Ryu, T. Kurokura
Strawberry (Fragaria × ananassa) is an octoploid species with an estimated genome size of about 800 Mb. The entire genomes of seven strawberry cultivars, ‘Donner’, ‘Hokowase’, ‘Aiberry’, ‘Toyonoka’, ‘Sachinoka’, ‘Reikou’ and ‘Nyoho’, were sequenced in order to clarify the differences in genome structures among the cultivars bred in Japan. Genome sequences were obtained using PacBio Sequel II with one SMRT cell for each cultivar. The total lengths of the generated HiFi reads ranged from 23.1 to 31.4 Gb, representing 29-37x of the strawberry genome. De novo assembly was performed 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’) to 1,520.2 Mb (‘Aiberry’). Ratios of haplotig contigs against the total length of primary and haplotig contigs ranged from 37% (‘Hokowase’) to 46% (‘Aiberry’). The top 50 primary contig sequences in the length of ‘Reikou’ were compared with the previously reported haploid pseudomolecule sequences of ‘Reikou’ (FAN_r2.3, a-haploid). One-to-one correspondences were observed between many primary contig sequences and FAN_r2.3 sequences, indicating the presence of primary contig sequences assembled at the chromosomal level. The pan genomes obtained in this study will contribute to identification of genome structure differences among all strawberries, including those tested here.
Isobe, S., Shirasawa, K., Hirakawa, H., Hamano, M., Ryu, K. and Kurokura, T. (2023). Pan genome of strawberry cultivars in Japan. Acta Hortic. 1381, 15-18
DOI: 10.17660/ActaHortic.2023.1381.2
strawberry, whole genome, de novo assembly

Acta Horticulturae