ArticlePeerJ2023
CPJSdraw: analysis and visualization of junction sites of chloroplast genomes.
Article in PeerJ, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
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121 citing papers in PubMed, 149 citations in OpenAlex.
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- Genetic and metabolite diversity of Sundaland Heptapleurum (Araliaceae) insight into evolutionary and specialized metabolite.BMC plant biology · 2026Article
- Article
- Comparative chloroplast genomics of 22 species of Sida (Malvaceae) reveals structural conservation, adaptive evolution, and preliminary phylogenetic structure.BMC plant biology · 2026Article
- Complete chloroplast genomes of four Triumfetta species obtained from herbarium specimens: comparative analysis and identification of a synapomorphic inversion.Scientific reports · 2026Article
- Chloroplast Phylogenomics and Evolutionary History of the Alpine EndemicInternational journal of molecular sciences · 2026Article
- Complete Chloroplast Genomes ofEcology and evolution · 2026Article
- Complete chloroplast genome features and phylogenetic analysis of Clematis cadmia.Scientific reports · 2026Article
- Comparative plastome analyses reveal life-form-associated selection signatures in Orchidaceae.BMC plant biology · 2026Article
- Complete Chloroplast Genome of theEcology and evolution · 2026Article
- Comparative Organellar Genomics of Pellidae: Insights into Codon Usage, Nucleotide Diversity, and Structural Evolution.Plants (Basel, Switzerland) · 2026Article
- Plastome evolution and phylogenomics of Glycine (Leguminosae: Papilionoideae).BMC plant biology · 2026Article
- Taxonomic Studies on 10 Species Within the GenusEcology and evolution · 2026Article
- Evolutionary dynamics of the chloroplast genome in Daphne (Thymelaeaceae): comparative analysis with related genera and insights into phylogenetics.FEBS open bio · 2026Article
61 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Chloroplast genomes are usually circular molecules, and most of them are tetrad structures with two inverted repeat (IR) regions, a large single-copy region, and a small single-copy region. IR contraction and expansion are among the genetic diversities during the evolution of plant chloroplast genomes. The only previously released tool for the visualization of junction sites of the regions does not consider the diversity of the starting point of genomes, which leads to incorrect results or even no results for the examination of IR contraction and expansion. Results: In this work, a new tool named CPJSdraw was developed for visualizing the junction sites of chloroplast genomes. CPJSdraw can format the starting point of the irregular linearized genome, correct the junction sites of IR and single-copy regions, display the tetrad structure, visualize the junction sites of any number (≥1) of chloroplast genomes, show the transcription direction of genes adjacent to junction sites, and indicate the IR expansion or contraction of chloroplast genomes. Conclusions: CPJSdraw is a software that is universal and reliable in analysis and visualization of IR expansion or contraction of chloroplast genomes. CPJSdraw has more accurate analysis and more complete functions when compared with previously released tool. CPJSdraw as a perl package and tested data are available at http://dx.doi.org/10.5281/zenodo.7669480 for English users. In addition, an online version with a Chinese interface is available at http://cloud.genepioneer.com:9929/#/tool/alltool/detail/335.
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