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

Abstract

Fragaria vesca, commonly known as wild or woodland strawberry, is the most widely distributed diploid Fragaria species and is native to Europe and Asia. Because of its small plant size, low heterozygosity, and relatively easy for genetic transformation, F. vesca 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 de novo assembled and annotated a telomere-to-telomere, gap-free genome of F. vesca ‘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 7 centromeres were annotated within the 7 chromosomes. Among the three previously recognized wild diploid strawberry ancestors, F. vesca, F. iinumae, and F. viridis, phylogenomic analysis showed that F. vesca and F. viridis are the ancestors of the cultivated octoploid strawberry F. × ananassa, and F. vesca is its closest relative. Three subgenomes of F. × ananassa belong to the F. vesca group, and one is sister to F. viridis. We anticipate that this high-quality, telomere-to-telomere, gap-free F. vesca genome, combined with our phylogenomic inference of the origin of cultivated strawberry, will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.

Telomere Length in Plants Estimated with Long Read Sequencing

“…This shows the significant differences and potential issues when using historic methods to estimate telomere length; it's possible that reported telomere lengths based on older methods are inaccurate thus muddying the comparison across data types. Recent T2T assemblies have been generated using combinations of Oxford Nanopore, PacBio HiFi, Bionano, and Illumina data with published telomere lengths for many plants: Glycine max Zhonghuang 13 (Zhang et al, 2023) , Citrullus lanatus G42 (Deng et al, 2022), Fragaria vesca (Zhou et al, 2023), Momordica charantia L. var. abbreviata Ser.…”

“…Recent T2T assemblies have been generated using combinations of Oxford Nanopore, PacBio HiFi, Bionano, and Illumina data with published telomere lengths for many plants: Glycine max Zhonghuang 13 (Zhang et al ., 2023), Citrullus lanatus G42 (Deng et al ., 2022), Fragaria vesca (Zhou et al ., 2023), Momordica charantia L. var. abbreviata Ser.…”

RepeatOBserver: tandem repeat visualization and centromere detection

“…Chromosomes are the black dots, Shannon diversity is plotted in red and the histograms are plotted in light blue. Species included are: Mouse-ear cress - A. thaliana (COLCEN assembly) (Naish et al, 2021), Human - Homo sapiens, Fruit fly - Drosophila pseudoobscura lowei (Bracewell et al ., 2019), Rice - Oryza sativa (Japonica Group) (Nawaz et al ., 2014), Turnip - Brassica rapa (Zhang et al ., 2023), Strawberry - Fragaria vesca (Zhou et al ., 2023), Sunflower - H. annuus (HA412) (Huang et al, 2022), Tomato - Solanum lycopersicum (Su et al ., 2021), Chicken - Gallus gallus domesticus (Piégu et al ., 2018), Mouse - Mus musculus (Hughes et al ., 2007), and Maize - Zea mays (Jiao et al ., 2017).…”

“…Although centromeres are both genetically and epigenetically determined, we find that natural centromere positions in most of the chromosomes that we explored could be determined based on the repetitiveness of the underlying genetic sequence without the need for epigenetic information. (Naish et al, 2021), Human -Homo sapiens, Fruit fly -Drosophila pseudoobscura lowei (Bracewell et al, 2019), Rice -Oryza sativa (Japonica Group) (Nawaz et al, 2014), Turnip -Brassica rapa (Zhang et al, 2023), Strawberry -Fragaria vesca (Zhou et al, 2023), Sunflower -H. annuus (HA412) (Huang et al, 2022), Tomato -Solanum lycopersicum (Su et al, 2021), Chicken -Gallus gallus domesticus (Piégu et al, 2018), Mouse -Mus musculus (Hughes et al, 2007), and Maize -Zea mays (Jiao et al, 2017).…”

CentIER: accurate centromere identification for plant genomes with sequence specificity information

“…The utilization of TRs to identify centromere regions is currently the primary basis for centromeric identification using bioinformatics approaches (Fu et al, 2023; Zhou et al, 2023). According to our results and previous studies, we found that some significant variations in the sequence of TRs across different chromosomes can be detected even within a same genome (Melters et al, 2013).…”