Pan-genome interface provides an in-depth analysis of Cucurbitaceae genomes. “Genome data” on this interface displays comprehensive information on pan-genome analyses for various species. Users can input data into a submission box to initiate specific queries.
Analysis methods:
| Part | Methods |
|---|---|
| Gene cluster | Protein sequences from all species were used as input for OrthoFinder software to construct gene families. A core cluster is defined as a cluster shared among all genomes. Clusters present in nearly all species, missing only one or two, were further classified as soft-core clusters. Clusters present in more than two but not all species, missing in several species, were defined as dispensable clusters. Specific clusters were those present in only one species. To further mimic the number of protein-coding genes in the pan-genome and core genome, we used PanGP (v1.0.1) using a completely random algorithm to set the sample size to 2000 and sample replicates to 80 based on OrthoFinder results. |
| Structural variation | Pairwise genome alignments between potato and tomato were conducted using the nucmer program in MUMmer (v.4.0.0beta2)[1]. SV detection was performed using SVMU (v.0.4-alpha)[2] to generate CNVs, insertions, and deletions. For SV calling, minimap2 (v.2.21-r1071)[3] was used to generate paired genome alignments, which were then passed to SyRI (v.1.2)[4] to identify and retain SVs, including insertions, deletions, SNPs, inversions, and translocations. We used different chromosome level varieties of Cucumis_sativus, Cucumis_melo, and Citrullus_lanatus to detect structural variations between them, and dynamically displayed SyRi results on the website. |