GDS: A Genomic Database for Strawberries (Fragaria spp.)

Abstract

Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries.

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

“…In summary, the gap-free F. vesca assembly reported here represents an important milestone in the assembly of diploid strawberry genome sequences. The complete genomic resource, together with our recently established strawberry genome database [ 24 ], will assist horticultural researchers in identifying genetic markers, investigating gene functions, and translating findings into genetic improvements in Fragaria .…”

Genomics and Biotechnology Empower Plant Science Research

“…However, genomic data have not been effectively utilized. To address this gap and efficiently utilize big data, Zhou et al [11] established the first multi-omics database focused on strawberries, storing all available genomic and transcriptomic data. They developed a series of bioinformatics tools, creating an integrated platform that will facilitate genetic and breeding research in strawberries.…”