Database

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

Wonhoon Lee^3,1,2†, Jongsun Park^3,4,5,6†, Jaeyoung Choi^3,4,6, Kyongyong Jung^3,4, Bongsoo Park⁷, Donghan Kim^3,4,6, Jaeyoung Lee¹, Kyohun Ahn⁴, Wonho Song⁴, Seogchan Kang⁷, Yong-Hwan Lee^3,4,8,5,6* and Seunghwan Lee^3,1,2*

• * Corresponding authors: Yong-Hwan Lee yonglee@snu.ac.kr - Seunghwan Lee seung@snu.ac.kr

• † Equal contributors

Author Affiliations

¹ Insect Biosystematics Laboratory, Seoul National University, Seoul 151–921, Korea

² Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151–921, Korea

³ Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Korea

⁴ Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151–921, Korea

⁵ Center for Fungal Pathogenesis, Seoul National University, Seoul 151–921, Korea

⁶ Center for Fungal Genetic Resources, Seoul National University, Seoul 151–921, Korea

⁷ Department of Plant Pathology, Penn State University, University Park, PA 16802, USA

⁸ Center for Agricultural Biomaterials, Seoul National University, Seoul 151–921, Korea

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BMC Genomics 2009, 10:148 doi:10.1186/1471-2164-10-148

Published: 7 April 2009

Abstract

Background

Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data.

Results

The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs.

Conclusion

The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site http://www.imgd.org/ webcite.