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

**Yuhan Zhou 1, Yushan Qiao 1, Zhiyou Ni 1, Jianke Du 1, Jinsong Xiong 1, Zongming Cheng 1,\* and Fei Chen 2,\***


**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.

**Keywords:** strawberry; bioinformatics; database; genome

## **1. Introduction**

Strawberries (*Fragaria* spp.), comprising of approximately 25 species [1], are plants from the Rosaceae. Their ploidy types range from diploid to decaploid [2,3], while wild members of the genus distributed throughout the northern hemisphere and parts of western South America [4]. The main cultivated and commercial strawberry species is the octoploid *Fragaria* ×*ananassa* (2n = 8x = 56) [5–8]. The first strawberry genome sequence from woodland strawberry (*Fragaria vesca*) was released in 2010 [9]. Since then, more and more strawberry species have been sequenced and annotated. In 2013, the cultivated strawberry (*Fragaria* ×*ananassa*) genome was sequenced using the Illumina and Roche 454 sequencing platforms [10], and was re-sequenced using a combination of short- and long-read approaches, producing a higher-quality assembly [11]. Strawberry genomics research not only promotes our understanding of the origin and evolution of strawberries but also has benefits for strawberry breeding [12].

Given these recent advances in strawberry genomics, it is necessary to establish a free online resource center for the integration of strawberry genome data. Therefore, we integrated the genomes and other related data of eight strawberry species (*Fragaria* ×*ananassa*, *Fragaria iinumae*, *Fragaria nilgerrensis*, *Fragaria nipponica*, *Fragaria nubicola*, *Fragaria orientalis*, *Fragaria vesca*, and *Fragaria viridis*) referring to the databases of other species, such as Arabidopsis, kiwifruit, and walnut [13–19]. We excavated, analyzed, and appropriately clustered these data into the online platform Genome Database for Strawberry (GDS). The GDS provides a user-friendly web interface; it also integrates a series of practical bioinformatics tools that enable researchers to search, browse, or retrieve specific information.

**Citation:** Zhou, Y.; Qiao, Y.; Ni, Z.; Du, J.; Xiong, J.; Cheng, Z.; Chen, F. GDS: A Genomic Database for Strawberries (*Fragaria* spp.). *Horticulturae* **2022**, *8*, 41. https:// doi.org/10.3390/horticulturae8010041

Academic Editor: Young-Doo Park

Received: 28 November 2021 Accepted: 28 December 2021 Published: 31 December 2021

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Genomics, transcriptomics and proteomic technology has developed rapidly. The GDS developed here will greatly benefit future application of high-throughput and -omics technologies. In addition, our achievement provides a directly resource for strawberry breeders and research communities, which will further facilitate the development of new strawberry cultivars with improved flavor. Nowadays, the phylogenomic relationships among the strawberry genomes is unclear. The current debate on the evolutionary of strawberries is one of the most important issues in the world. Our database could promote research on strawberry evolution.
