CPGView: A package for visualizing detailed chloroplast genome structures.

Chloroplast genomes have been widely used in studying plant phylogeny and evolution. Several chloroplast genome visualization tools have been developed to display the distribution of genes on the genome. However, these tools do not draw features, such as exons, introns, repetitive elements, and variable sites, disallowing in-depth examination of the genome structures. Here, we developed and validated a software package called Chloroplast Genome Viewers (CPGView). CPGView can draw three maps showing (i) the distributions of genes, variable sites, and repetitive sequences, including microsatellites, tandem and dispersed repeats; (ii) the structure of the cis-splicing genes after adjusting the exon-intron boundary positions using a coordinate scaling algorithm, and (iii) the structure of the trans-splicing gene rps12. To test the accuracy of CPGView, we sequenced, assembled, and annotated 31 chloroplast genomes from 31 genera of 22 families. CPGView drew maps correctly for all the 31 chloroplast genomes. Lastly, we used CPGView to examine 5998 publicly released chloroplast genomes from 2513 genera of 553 families. CPGView succeeded in plotting maps for 5882 but failed to plot maps for 116 chloroplast genomes. Further examination showed that the annotations of these 116 genomes had various errors needing manual correction. The test on newly generated data and publicly available data demonstrated the ability of CPGView to identify errors in the annotations of chloroplast genomes. CPGView will become a widely used tool to study the detailed structure of chloroplast genomes. The web version of CPGView can be accessed from http://www.1kmpg.cn/cpgview.