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    • Figure 1. 

      Data management strategy centered on a data unit consisting of one genome and its annotation. (a) Automated and standardized features of database management. (b) Structure and components of the database directory tree.

    • Figure 2. 

      SGH is designed around the integration of data and analytical functions, and its overall framework is AI-ready.

    • Figure 3. 

      Interface design and functional overview of SGH. (a) Overview of the main interface. The left panel shows the directory tree for managing genome versions. The right panel shows genome assembly and related information, with the corresponding function buttons below. (b) Overview of the genome data exploration functions in SGH.

    • Figure 4. 

      Genome data exploration functions and representative outputs supported by SGH. (a) Four classes of functions supported by the genome database. (b) Sequence alignment and phylogenetic tree construction, (c) gene structure analysis, (d) functional enrichment analysis of gene sets, (e) single gene expression pattern analysis, and (f) multiple gene expression pattern analysis, respectively.

    • Figure 5. 

      Genome synteny analysis and visualization supported by SGH. (a) Comparative genomics module of SGH. (b) Rapid Circos visualization of genomic features and (c) synteny information. (d) Genome synteny analysis and visualization between two species. The synteny output, namely the Link Info. File, provides an interface that can be automatically recognized and called by other functions. (e) Flexible layout and (f) visualization of synteny across multiple species.

    • Figure 6. 

      Identification and evolutionary analysis of CAX genes in three pineapple germplasm accessions. Phylogenetic trees of CAX genes in (a) 'BL', (b) 'GP', and (c) 'LY', respectively, based on protein homology search results using XM_020241177 as the reference. (d) Expression levels of five candidate CAX genes in the flesh of normal fruit and mild watercore fruit in 'GP'. (e) Genomic Circos plot of 'GP'. From the inner to outer tracks, the plot shows the synteny links, GC content, gene density, and chromosomal positions of the five candidate CAX genes. (f) Synteny analysis of CAX genes among the three pineapple genomes.