Introduction of IMGD
The mitochondrial genome in Hexapoda, generally called .Insect., is generally around 15 kilobases (kb) in length and encodes 37 genes: 13 protein coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs). Short fragment sequences in this genome has been used as phylogenetic markers to explain the evolutionary relationships at species, genus, or family level. Gene arrangements of the 37 genes have been also provided as an ideal tool for intraphylum, class, or order evolutionary analyses. Recently two databases, AMiGA and MiTOME, archived Athropoda and metazoa mitochondrial genomes, respectively with web-based interface. However, adequate phylogenetic tools for in-depth analyses will be needed.
For overcoming the shortage, we developed new insect mitochondrial genome database (IMGD; http://www.imgd.org/), providing not only 114 mitochondrial genome database and 86,708 mitochondrial gene elements covering 21,605 insect species, but also multifaceted web-based phylogenetic tools. As considering the maintenance of IMGD, the standardized genome database structure implemented in Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr; Part et al., 2008) was used. Based on this, basic features of mitochondrial genomes, such as length, GC ratio and AT-skew, were displayed. And sequences of each gene elements, such as PCGs, tRNAs and rRNAs, was shown via Mitochondrial Genome Browser in IMGD. For 86,708 mitochondrial gene elements, we developed the simple annotation pipeline using InterPro Scan, so that all elements are categorized in each type on the web.
Recently, phylogenetic analyses required different tree-generated methods for confirming reliability of analyses. For drawing many phylogenetic tress using insect mitochondrial gene sequences coverging various range of species, web-based phylogenetic tools which connected to IMGD directly will be needed. For satisfying this requirement, Phyloviewer, which is newly developed web-based tool covering from multiple sequence alignment to decoration of phylogenetic tree on the web (http://www.phyloviewer.org; Park et al., unpublished), was implemented. Phyloviewer supports six different programs, such as ClustalW, DNAML, PROML, DNAPARS, PROTPARS and Phyml, supporting three different methods, Neighbor-joining (NJ), Maximum Likelihood (ML) and Maximum Parsimony (MP) with bootstrapped option. For executing these programs, you can use new user interface, termed as Species-driven User Interface (SUI) which provides selecting species via taxa and running eight useful functions with selected targets (Fig 1). SUI will give researchers easy way to manipulate various levels of species.
For more in-depth analyses, IMGD provide the gateway to CFGP serving six useful bioinformatic tools and many analyses tools. Via Object Browser, users can collect sequences or species itself, in consequence, diverse analyses will be conducted in CFGP web site.
With these functions, IMGD can be good resource for insect mitochondrial gene analyses. We will do our best for updating latest sequence information and maintaining IMGD system.