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.

Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae)

“…It originates in Southwest China, but now is widely dispersed in the temperate zone of Northern Hemisphere, mostly occurring on sunny mountain slopes or on the sides of ravines with an elevation of 300-1200 m (Chen et al genome of Prunus persica (HQ336405) (Jansen et al 2011) was used as the initial reference as well as for the purpose of genome annotation. A physical map of the genome was drawn with the web-based tool OrganellarGenomeDraw (OGDRAW) (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al 2013).…”

The complete chloroplast genome of a rare orchid species Liparis loeselii (L.)

“…A physical map of the plastome was generated using OGDRAW (http://ogdraw.mpimp-golm. mpg.de/) (Lohse et al 2013). …”

Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

“…Физическая карта пластидного генома A. sativum была построена с помощью программы OGDRAW (рис. 1) (Lohse et al, 2013). Границы инвертиро-ванных повторов были перепроверены секвенированием с праймерами, специфичными к фланкирующим участ-кам: ycf1-ndhF (5′-ATTGGTATTATTCTGGATACGGC-3′; 5′-GATCTGTTTATTCATCTCTACAG-3′), rpl22-rpl2 (5′-GATGCTCGATAAGGCATAAG-3′; 5′-GTAAGCG TCCTGTAGTAAG-3′), rpl2-psbA (5′-CTGTAGTAAGAG GAGTAGT-3′; 5′-TTGATAGTCAAGGTCGTGT-3′).…”