OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

Abstract

Mitochondria and plastids (chloroplasts) are cell organelles of endosymbiotic origin that possess their own genetic information. Most organellar DNAs map as circular double-stranded genomes. Across the eukaryotic kingdom, organellar genomes display great size variation, ranging from ∼15 to 20 kb (the size of the mitochondrial genome in most animals) to >10 Mb (the size of the mitochondrial genome in some lineages of flowering plants). We have developed OrganellarGenomeDraw (OGDRAW), a suite of software tools that enable users to create high-quality visual representations of both circular and linear annotated genome sequences provided as GenBank files or accession numbers. Although all types of DNA sequences are accepted as input, the software has been specifically optimized to properly depict features of organellar genomes. A recent extension facilitates the plotting of quantitative gene expression data, such as transcript or protein abundance data, directly onto the genome map. OGDRAW has already become widely used and is available as a free web tool (http://ogdraw.mpimp-golm.mpg.de/). The core processing components can be downloaded as a Perl module, thus also allowing for convenient integration into custom processing pipelines.

Figure 1.

Chart illustrating the workflow of OGDRAW. Cyan fields indicate user input, yellow fields denote steps performed by OGDRAW. See text for details.

Figure 2.

Map of the tomato (Solanum lycopersicum) chloroplast genome. The map was drawn using the complete genome sequence as input ((23); GenBank accession number NC_007898.2). The gray arrows indicate the direction of transcription for the two DNA strands. The circle inside the GC content graph marks the 50% threshold.

Figure 3.

Visualization of a gene expression data set on the physical map of the tomato (S. lycopersicum) chloroplast genome. The expression data are from a polysome profiling experiment (see text for details).