Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels

Abstract

Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa)

“…Analysis of strawberry pangenomes also resulted in interesting findings about strawberry evolution and domestication. Based on transposable element analysis of a pangenome constructed from 10 high-quality strawberry genomes, Lyu et al (2023) suggested that Fragaria viridis may not be one of the diploid Fragaria ×ananassa ancestors as previously thought. Additionally, Qiao et al (2021) discovered a new diploid strawberry species during assembly of their own pangenome.…”

“…Evolutionary analysis of Fragaria ×ananassa suggested genomic contributions of four diploid progenitor species: Fragaria vesca, Fragaria iinumae, Fragaria viridis, and Fragaria nipponica (Edger et al, 2019;2020). However, analysis from other groups has suggested that both F. viridis and F. nipponica are not among the diploid progenitors (Liston et al, 2020;Jin et al, 2023;Lyu et al, 2023;Session and Rokhsar, 2023). As identification of the progenitor species may enable greater prediction of polyploid responses to environmental stress and climate change (Liston et al, 2020), further analysis of the evolutionary history of strawberry will be necessary to confirm the identities of the diploid progenitor species.…”