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

Wonhoon Lee; Jongsun Park; Jaeyoung Choi; Kyongyong Jung; Bongsoo Park; Donghan Kim; Jaeyoung Lee; Kyohun Ahn; Wonho Song; Seogchan Kang; Yong Hwan Lee; Seunghwan Lee

doi:10.1186/1471-2164-10-148

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

Wonhoon Lee
, Jongsun Park
, Jaeyoung Choi
, Kyongyong Jung
, Bongsoo Park
, Donghan Kim
, Jaeyoung Lee
, Kyohun Ahn
, Wonho Song
, Seogchan Kang
, Yong Hwan Lee
, Seunghwan Lee

Research output: Contribution to journal › Article › peer-review

17 Citations (Scopus)

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 newintegrated 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.

Original language	English
Article number	148
Journal	BMC Genomics
Volume	10
DOIs	https://doi.org/10.1186/1471-2164-10-148
Publication status	Published - 7 Apr 2009

Bibliographical note

Funding Information:
This research was supported by Korea Ministry of Environment as "The Eco-technopia 21 project", a grant from by Agricultural R&D Promotion Center, and a grant from Biogreen21 Project (20070301034032) to S.L. It was also supported by a grant from Crop Functional Genomics Center (CG1141), Korean Research Foundation Grant (KRF-2006-005-J04701), Biogreen21 Project (20080401034044) funded by Rural Development Administration and the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MEST) (R11-2008-062-03001-0) to Y.H.L. J.P. acknowledges a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project.

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10.1186/1471-2164-10-148

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title = "IMGD: An integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes",

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 newintegrated 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.",

author = "Wonhoon Lee and Jongsun Park and Jaeyoung Choi and Kyongyong Jung and Bongsoo Park and Donghan Kim and Jaeyoung Lee and Kyohun Ahn and Wonho Song and Seogchan Kang and Lee, \{Yong Hwan\} and Seunghwan Lee",

note = "Funding Information: This research was supported by Korea Ministry of Environment as {"}The Eco-technopia 21 project{"}, a grant from by Agricultural R\&D Promotion Center, and a grant from Biogreen21 Project (20070301034032) to S.L. It was also supported by a grant from Crop Functional Genomics Center (CG1141), Korean Research Foundation Grant (KRF-2006-005-J04701), Biogreen21 Project (20080401034044) funded by Rural Development Administration and the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MEST) (R11-2008-062-03001-0) to Y.H.L. J.P. acknowledges a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project.",

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doi = "10.1186/1471-2164-10-148",

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T2 - An integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

AU - Lee, Wonhoon

AU - Park, Jongsun

AU - Choi, Jaeyoung

AU - Jung, Kyongyong

AU - Park, Bongsoo

AU - Kim, Donghan

AU - Lee, Jaeyoung

AU - Ahn, Kyohun

AU - Song, Wonho

AU - Kang, Seogchan

AU - Lee, Yong Hwan

AU - Lee, Seunghwan

N1 - Funding Information: This research was supported by Korea Ministry of Environment as "The Eco-technopia 21 project", a grant from by Agricultural R&D Promotion Center, and a grant from Biogreen21 Project (20070301034032) to S.L. It was also supported by a grant from Crop Functional Genomics Center (CG1141), Korean Research Foundation Grant (KRF-2006-005-J04701), Biogreen21 Project (20080401034044) funded by Rural Development Administration and the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea government (MEST) (R11-2008-062-03001-0) to Y.H.L. J.P. acknowledges a graduate fellowship provided by the Ministry of Education through the Brain Korea 21 Project.

PY - 2009/4/7

Y1 - 2009/4/7

N2 - 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 newintegrated 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.

AB - 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 newintegrated 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.

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DO - 10.1186/1471-2164-10-148

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VL - 10

JO - BMC Genomics

JF - BMC Genomics

M1 - 148

ER -

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

Abstract

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