Visualization of Oligonucleotide-Based Probes Along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos)

Methods Mol Biol. 2023:2672:409-444. doi: 10.1007/978-1-0716-3226-0_26.

Abstract

Fluorescence in situ hybridization (FISH) using oligonucleotide-based probes is an innovative modification of classic FISH techniques, enabling karyotypic identifications. Here, we exemplarily describe the design and in silico visualization of oligonucleotide-based probes derived from the Cucumis sativus genome. Additionally, the probes are also plotted comparatively to the closely related Cucumis melo genome. The visualization process is realized in R using various libraries for linear or circular plots including RIdeogram, KaryoploteR, and Circlize.

Keywords: Comparative genomics; FISH; Hybrid genomes; Oligo-FISH; Phylogenomics; R; Visualization.

MeSH terms

  • Cucumis sativus* / genetics
  • Genome*
  • In Situ Hybridization, Fluorescence
  • Oligonucleotide Probes / genetics
  • Oligonucleotides / genetics

Substances

  • Oligonucleotide Probes
  • Oligonucleotides