Abstract
Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.
Highlights
Organellar genomes display relatively conserved gene contents, are usually transmitted uniparentally and are, excluded from sexual recombination
The mitochondrial and plastid genomes are small and occur in many copies per cell, which makes them convenient and cheap targets of sequencing projects [1,2,3]. These properties make organellar genomes extremely informative in resolving taxonomic relationships, and it can be expected that the enormous increase in published organellar genome sequences will continue for the foreseeable future [2,3]
There are many assembly methods and pipelines [e.g., GetOrganelle [4] or IOGA [5]], and we are currently aware of no less than twelveautomatic annotation tools for organellar genomes (6–15, https://git.metabarcoding.org/org-asm/org-annotate, http://megasun.bch.umontreal.ca/cgi-bin/mfannot/ mfannotInterface.pl). These range from specialized applications such as MITOS [11], that were designed for a subset of organellar genomes and whose output requires little to no quality control or manual curation, to GeSeq, a flexible tool that allows the annotation of essentially any organellar genome [15]
Summary
Organellar genomes display relatively conserved gene contents, are usually transmitted uniparentally (most often maternally) and are, excluded from sexual recombination. There are many assembly methods and pipelines [e.g., GetOrganelle [4] or IOGA [5]], and we are currently aware of no less than twelve (semi)automatic annotation tools for organellar genomes (6–15, https://git.metabarcoding.org/org-asm/org-annotate, http://megasun.bch.umontreal.ca/cgi-bin/mfannot/ mfannotInterface.pl). Before the launch of OrganellarGenomeDRAW (OGDRAW) in 2007 [17] and GenomeVx in 2008 [18], organelle genome maps were often drawn manually, lacked a homogeneous design and were inconsistent in feature display These shortcomings were overcome by the two programs and OGDRAW quickly became the standard in the field. As described in detail below, in the course of the movement of OGDRAW to its new environment, we added several new features to the program (in its new version 1.3.1) and fixed known bugs
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