Case Study写作

Case study

To illustrate the application of the SoIR database, we present a case study on the identification of structural variations. Inversions serve as significant catalysts for local adaptation and diversification by protecting inverted sequences from recombination. Our study identified structural variations in seven potato varieties, documenting a total of 623 inversions, with 70 of these exceeding 1 Mb in size. Initial comparisons using the potato structural variation interface (Figure 4A) revealed that the DM8 variety exhibited inversions at approximately DMchr03:43.39–49.29Mb relative to four other potato samples (E4-63, E86-69, RH, RH10-5) (Figure 4B), consistent with previous reports in Nature (1). By selecting the inverted region, users can access detailed gene information within this segment (Figure 4A), allowing for in-depth analysis of gene functions, as shown in Figure 4. Clicking on a gene initiates a search in the database, leading to a dedicated results page (Figure 4C). Notably, this inversion region contained 520 genes associated with carotenoid content in tubers (1). Our database identified the gene ‘DM8C03G19260.1’ in the DM8 genome, located near the inversion breakpoint, which was homologous to the ‘Soltu.DM.03G018410’ gene in the DM6.1 version, also linked to carotenoid content (1). The database provides comprehensive information on this gene, including its sequence, structure, functionality and associated TFs (Figure 4C). It further details gene functional annotations, CRISPR applications, synteny genes, RNA sequencing data, homologs and gene duplication types (Figure 4D). Moreover, users can easily access online analytical tools with a single click, where gene sequences are pre-populated for further analysis.