Genome-wide discovery of DNA variants in cucumber somaclonal lines

Molecular insight into somaclonal variation phenomena from transcriptome profiling of cucumber (Cucumis sativus L.) lines

“…The principal component analysis was performed using R package with "ggplot2" package. Identified DEGs were compared with previously obtained genome sequencing data for somaclonal lines (BioProject PRJNA563814) (Skarzyńska et al 2020) to locate single-nucleotide variations (SNVs) within the gene structure or upstream region (1500 bp upstream from the start codon). To visualize the DEGs position across chromosome maps, MapChart software (Voorrips 2002) and the R package "circlize" (Gu et al 2014) were applied.…”

“…The PlantCARE database (http://bioin forma tics.psb.ugent .be/webto ols/plant care/html/) was accessed to estimate cis-acting elements and the possible functional influence of transcription factors (TF). The STRING algorithm (version 10.5) (Szklarczyk et al 2017), using Arabidopsis thaliana as a model, was applied for an additional analysis of the possible interactions between the selected proteins coded by DEGs and genes affected by SNVs (G_SNVs) ( Table S3), which were previously selected (Skarzyńska et al 2020).…”

“…We performed a comparison of previously detected SNVs within the cucumber genome (Skarzyńska et al 2020) with DEGs across the genome of the somaclonal lines. Taking into consideration the number of genes with SNVs across the gene structure (exon and intron) and upstream region (− 1500 bp), the highest number of DEGs were observed in the S3 line-99, whereas 37 and 38 were observed in the S1 and S2 lines, respectively ( Table 2).…”

“…The S3 line produced shoot apices yellow-green in color. The phenotypic differences in the somaclonal lines are predominantly associated with the constituent factors and explants from which the culture was initiated (Skarzyńska et al 2020).…”

“…In addition, we determined the chromosomal location of the genes to assess whether a specific genome region is more frequently subjected to rearrangements or whether the changes are randomly distributed across the genome. Based on findings from a previous comparative genomics study (Skarzyńska et al 2020), we also determined genes that may be affected by structural polymorphisms, and how genomic variants influence gene expression and protein-protein molecular networks in the somaclones.…”