ArticleFrontiers in genetics2020
Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes.
Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 250 papers.
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250 citing papers in PubMed.
- Evolutionary dynamics of the chloroplast genome in Abutilon (Malvoideae, Malvaceae).BMC plant biology · 2026Article
- Complete plastome data of rareData in brief · 2026Article
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- Structural characteristics of the Phoebe hui chloroplast genome and phylogenetic analyses of Phoebe plants.BMC genomics · 2026Article
- Chloroplast Genome Characterization, Comparative Analysis, and Phylogenetic Insights into FiveInternational journal of molecular sciences · 2026Article
- Characterization and comparative analysis of the complete chloroplast genomes of twelve Allium species from Kazakhstan.Scientific reports · 2026Article
- Complete mitochondrial genome ofMicrobiology resource announcements · 2026Article
- Complete chloroplast genomes of four Triumfetta species obtained from herbarium specimens: comparative analysis and identification of a synapomorphic inversion.Scientific reports · 2026Article
- Complete mitochondrial genome ofMicrobiology resource announcements · 2026Article
- Comparative chloroplast genomics of 22 species of Sida (Malvaceae) reveals structural conservation, adaptive evolution, and preliminary phylogenetic structure.BMC plant biology · 2026Article
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- Complete Mitochondrial Genome ofGenes · 2026Article
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- Chloroplast genome comparison, phylogeny, and molecular evolution of five endemic Potentilla (Rosaceae) species in Mongolia.Genetica · 2026Article
- Sequence decoding and analysis of the first reference mitogenome of globally threatened clown-knife fish, Chitala chitala: witness of codon usage bias and intense purifying selection.Molecular biology reports · 2026Article
- Complete mitochondrial genome ofMicrobiology resource announcements · 2026Article
- Complete Chloroplast Genomes ofEcology and evolution · 2026Article
- Comparative Chloroplast Genomics ofEcology and evolution · 2026Article
190 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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