The Browse interface enhances user interaction with genomic analysis results. It includes sections on genome synteny, transcription factors (TF), and key functional genes. The “Genome synteny” tool constructs syntenic diagrams for both intraspecies and interspecies loci at the chromosome level, including syntenic dot plots and diagrams. Users can select and view specific syntenic diagram genes or blocks.
Analysis methods:
| Part | Methods |
|---|---|
| Genome synteny | Dotplot: After conducting alignments using BLAST+ (version 2.16.0, E value < 1e−5; identity > 60%; score > 150), we proceeded to utilize D3.js for visualization within our database. Synteny: After conducting a gene collinearity analysis using MCScanX[1] with default parameters, the results can be visualized within the database using D3.js. Detailed examples can be found on GitHub. |
| Expansion/Contraction | Multiple sequence comparisons of genes in single-copy gene families were performed using MUSCLE, and phylogenetic trees were constructed from maximum likelihood models using RaxML[2]. Single-copy gene families combined with species trees were used to estimate divergence times via the r8s method[3]. Time correction nodes were obtained from the Timetree database[4]. Single-copy and multicopy gene families were detected by cluster analysis with the MCL graph clustering algorithm, and those with similar gene sequences usually belonged to one gene family. The output of the parsed MCL was used as an input file for the CAFE software[5] for the analysis of contraction and expansion of gene families. |
| Functional genes | The 41 anthocyanin genes of Arabidopsis were obtained from the BRAD website[6]. Homologous flowering, anthocyanin genes in other vegetable species were identified by BLASTP (E value < 1e−5; identity > 60%; score > 150) via manual checking. Identifying hormones using blast and pfam (Comparison Table). Furthermore, resistance gene analogs were detected in 81 Solanaceae species using the pipeline of RGAugury[7]. |
| Transcription factors | Transcription factor (TF) families were identified online using the PlantTFDB website[8]. |
| Methylation | Methylation genes were detected by the accession number of the Pfam[9] annotation. (Comparison Table) |