The telomere-to-telomere genome of <i>Fragaria vesca</i> reveals the genomic evolution of <i>Fragaria</i> and the origin of cultivated octoploid strawberry

Abstract

<i>Fragaria vesca,</i> commonly known as wild or woodland strawberry, is the most widely distributed diploid <i>Fragaria</i> species and is native to Europe and Asia. Because of its small plant size, low heterozygosity, and relative ease of genetic transformation, <i>F. vesca</i> has been a model plant for fruit research since the publication of its Illumina-based genome in 2011. However, its genomic contribution to octoploid cultivated strawberry remains a long-standing question. Here, we <i>de novo</i> assembled and annotated a telomere-to-telomere, gap-free genome of <i>F. vesca</i> 'Hawaii 4', with all seven chromosomes assembled into single contigs, providing the highest completeness and assembly quality to date. The gap-free genome is 220 785 082 bp in length and encodes 36 173 protein-coding gene models, including 1153 newly annotated genes. All 14 telomeres and seven centromeres were annotated within the seven chromosomes. Among the three previously recognized wild diploid strawberry ancestors, <i>F. vesca</i>, <i>F. iinumae</i>, and <i>F. viridis</i>, phylogenomic analysis showed that <i>F. vesca</i> and <i>F. viridis</i> are the ancestors of the cultivated octoploid strawberry <i>F.</i> × <i>ananassa</i>, and <i>F. vesca</i> is its closest relative. Three subgenomes of <i>F.</i> × <i>ananassa</i> belong to the <i>F. vesca</i> group, and one is sister to <i>F. viridis</i>. We anticipate that this high-quality, telomere-to-telomere, gap-free <i>F. vesca</i> genome, combined with our phylogenomic inference of the origin of cultivated strawberry, will provide insight into the genomic evolution of <i>Fragaria</i> and facilitate strawberry genetics and molecular breeding.