*3.15. Download*

The Download module provides access to the genome assembly, CDS and PEP sequences, annotation data, and miRNA downloads in FASTA and GFF3 formats. Chloroplast genomes of seven strawberry species and related publications are also available. We implemented an FTP site to store and share the data, which users can download at a rapid speed.

#### *3.16. Community of Strawberry Researchers*

In the Community module, we provided links to 39 horticultural conferences and 11 relevant publications on strawberry genome research. We also included an FAQ section to explain how to use the database and a contact list for the researchers who established it.

#### **4. Discussion**

The rapid development of genome sequencing technology has enabled the sequencing, assembly, and annotation of many plant genomes, providing genetic information on plant growth, development, and evolution. Genome sequencing and analysis technologies have not only deepened our understanding of plant species but also accelerated gene functional studies and molecular breeding. There are many strawberry species and varieties with complicated genomes, and their genome data are refined and updated very often. For example, the *Fragaria vesca* genome (214.4 Mb) was the first sequenced strawberry genome [10]. However, its quality was not ideal. Later on, Edger and associates from the University of California sequenced the genome of woodland strawberry Hawaii-4 using single-molecule real-time (SMRT) sequencing [22] and constructed a more complete genome map (V4.0). The SMRT sequencing can produce much longer contigs, greatly facilitating genome assembly and annotation. Specifically, the length of contig N50 of V4.0 reached 7.9 Mb, 300 times longer than those of V1.0, and >99.8% of the contigs were successfully mapped to the seven chromosomes. This new strawberry genome map offers more accurate sequences and detailed location information. The polyploidization of strawberries, which contain diploid, tetraploid (*Fragaria orientalis*) [5], and octoploid (*Fragaria* ×*ananassa*) varieties, has made the sharing, analysis, and integration of their

genomic data a difficult task. A more convenient online database with multiple integrated and classified strawberry genomes is urgently needed. It will facilitate the gene-functional studies, thereby promoting the improvement of the yield and quality of strawberries [52]. To our knowledge, GDS is currently the only up-to-date database for strawberries that integrates multiple bioinformatics tools.

The storage and analysis of strawberry genome data are also hot research topics, and databases such as GDR (Genome Database for Rosaceae) and Kazusa (Strawberry garden) were created for these purposes. Although GDR and Kazusa have developed databases for strawberries, these databases have a number of problems that require urgent solutions. First, most of the genomic data are unprocessed and scattered. The data lack functional annotations, are not clustered in gene families, and are not preformatted for searching. After downloading data from these public databases, one must process the data oneself, which is a challenge for those with less expertise in bioinformatics. More importantly, some websites are difficult to access in China, and data downloads are also greatly restricted sometimes. To date, there is no specific, widely available database for strawberry research. Here, we use the latest version of the software for the analysis of strawberry proteins that are not all available on other websites. In addition, our laboratory specializes in strawberry research and has extensive collaboration with other strawberry research groups. In the future, newly released strawberry sequencing data will be updated in the database and made available to all researchers in a timely manner.

GDS stores the genome sequences of eight strawberry species and related gene annotations. The advanced and popular BLAST and JBrowse tools have been implemented, as well as a syntenic block search tool and an miRNA finder. This database serves as a central portal for the strawberry research community, enabling researchers to download genomes, protein sets, transcription data, and recently published articles on the strawberry genome. The GDS will be constantly updated when new genomes, transcriptomes, and other types of genetic datasets are published. In the future, we will develop and establish more gene online analysis tools to facilitate strawberry researchers in conducting online analysis. We will do our best to develop and deploy new omics tools in the GDS to provide a better user experience. Furthermore, GDS will contain studies and statistics on strawberries' breeding. In summary, this new database incorporates published strawberry plant genomes, multiple analysis tools, new features for strawberry plant genomic data analysis, gene function characterization, synteny and miRNA search, and publication, which is easily accessed and can potentially benefit the strawberry plant research community.

**Author Contributions:** Z.C. and F.C. designed and led this project. Y.Z. constructed the GDS. Y.Q., J.D., Z.N. and J.X. analyzed the data. Y.Z. wrote the draft manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** Fei Chen acknowledges funding from the Fundamental Research Fund for the Central University (KYXJ202004) and a starting fund from Nanjing Agricultural University (804012). Zongming Cheng and Jinsong Xiong acknowledge funding from Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). This work was supported by the National Natural Science Foundation of China (Grant no. 32072540, 31872056).

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** All code about the database is available on Github (https://github. com/Han-Oscar/GDS-code, accessed on 10 November 2021).

**Acknowledgments:** We thank Yushan Qiao, Zhiyou Ni, Jianke Du for valuable comments and suggestions on our database. We thank Xiaogang Lei and Xiaojiang Li for providing technical assistance to our database development and Fei Chen, Zongming Cheng for assistance with the correction of the English language in the manuscript.

**Conflicts of Interest:** The authors declare that they have no conflict of interest.
