Fragaria viridis YNU Genome v1.0 Assembly & Annotation
Qiao Q, Edger PP, Xue L, La Q, Lu J, Zhang YC, Alan EY, Adrian EP, Steven JK, Montagu MV, Van de Peer Y, Lei JJ, Zhang TC. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). 2021. Proceedings of the National Academy of Sciences Nov 2021, 118 (45) e2105431118; DOI: 10.1073/pnas.2105431118
Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past ten years. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome re-sequencing data for 128 additional accessions to estimate the genetic diversity and structure of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (F. emeiensis Lei). Lastly, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families associated with important agronomic traits. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These new reference genomes and datasets, combined with our new phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.
Homology of the Fragaria viridis Genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
Functional annotation for the Fragaria viridis Genome v1.0 are available for download below. The Fragaria viridis Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Fragaria viridis genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.