*3.11. Tracing Whole-Genome Duplication Using Synteny Browse Search*

Given the close phylogenetic relationships among strawberry species, there are likely to be many homologous gene blocks in their genomes. The Python version of MCScan [47] was used to identify homologous gene blocks in the genomes of the strawberry species. We selected four species (Figure 7), including cultivated strawberry, to use in searches of homologous genes, as well as upstream and downstream genes. Scientists can look for syntenic genes of *F. vesca* by entering a gene identifier, finding the homologous gene(s), and using them as input for a subsequent gene search.

#### *3.12. microRNA Search*

microRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules with a length of approximately 22 nucleotides that are encoded by endogenous genes. The Rfam database [48,49] is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures, and covariance models. The GDS use cmscan [50] from the Infernal (V1.1.4) software package to predict the miRNAs in the six species of strawberry with high-quality assemblies.


**Figure 7.** The synteny search tool in GDS is designed for whole-genome duplication analyses. Researchers can use Synteny Browse Search to look for syntenic genes by entering a gene identifier and selecting a number of flanking genes to be presented.

## *3.13. Transcription Factor Search*

Transcription factors play an important role in all biological processes, from seed germination to senescence. Therefore, it is critical for researchers to gain a good understanding of the relationship between the structures and functions of various transcription-factor families. iTAK [51] is a program that can identify plant transcription factors (TFs), transcriptional regulators (TRs), and protein kinases (PKs) based on protein or nucleotide sequences. It then classifies individual TFs, TRs, and PKs into different gene families. iTAK (v1.7) is used here to identify and analyze transcription factors from the six highly assembled strawberry species.

## *3.14. Gene Search*

From the search results of BLAST and JBrowse, scientists can enter a gene identifier to search for information about the gene version (Figure 8a), protein and CDS sequence (Figure 8b), KEGG annotation, gene family, signal peptides (Figure 8c), and GO annotation (Figure 8d). The results include links to the corresponding annotation databases for more information, as well as gene expression data (Figure 8e) from mature pollen.


**Figure 8.** Gene search tool in GDS. (**a**) Related information; (**b**) protein and CDS sequence; (**c**) KEGG annotation, gene family, and signal peptides; (**d**) GO annotation, and (**e**) expression.
