metaTIGER: a metabolic evolution resource

Metabolic networks are a subject that has received much attention, but existing web resources do not include extensive phylogenetic information. Phylogenomic approaches (phylogenetics on a genomic scale) have been shown to be effective in the study of evolution and processes like horizontal gene transfer (HGT). To address the lack of phylogenomic information relating to eukaryotic metabolism, metaTIGER (www.bioinformatics.leeds.ac.uk/metatiger) has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences were used to create a comprehensive database of 2257 maximum-likelihood phylogenetic trees, some containing over 500 organisms. The trees can be viewed using iTOL, an advanced interactive tree viewer, enabling straightforward interpretation of large trees. Complex high-throughput tree analysis is also available through user-defined queries, allowing the rapid identification of trees of interest, e.g. containing putative HGT events. metaTIGER also provides novel and easy-to-use facilities for viewing and comparing the metabolic networks in different organisms via highlighted pathway images and tables. metaTIGER is demonstrated through evolutionary analysis of Plasmodium, including identification of genes horizontally transferred from chlamydia.

[1]  Jinling Huang,et al.  Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? , 2007, Genome Biology.

[2]  Imre Vastrik,et al.  Reactome: a knowledgebase of biological pathways , 2004, OTM Workshops.

[3]  David James Sherman,et al.  Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts , 2005, Nucleic Acids Res..

[4]  A. Stead,et al.  Plasmodium falciparum: interaction of shikimate analogues with antimalarial drugs. , 2005, Experimental parasitology.

[5]  C. Claudel-Renard,et al.  Enzyme-specific profiles for genome annotation: PRIAM. , 2003, Nucleic acids research.

[6]  Jessica C Kissinger,et al.  Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum , 2004, Genome Biology.

[7]  Emmet A. O'Brien,et al.  TBestDB: a taxonomically broad database of expressed sequence tags (ESTs) , 2007, Nucleic Acids Res..

[8]  C W Roberts,et al.  A complete shikimate pathway in Toxoplasma gondii: an ancient eukaryotic innovation. , 2004, International journal for parasitology.

[9]  Debashish Bhattacharya,et al.  Horizontal gene transfer in chromalveolates , 2007, BMC Evolutionary Biology.

[10]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[11]  J. Pinney,et al.  metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella , 2005, Nucleic acids research.

[12]  J. Dopazo,et al.  The human phylome , 2007, Genome Biology.

[13]  Jessica C Kissinger,et al.  Mining the Plasmodium genome database to define organellar function: what does the apicoplast do? , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[14]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[15]  Philippa Rhodes,et al.  CryptoDB: a Cryptosporidium bioinformatics resource update , 2005, Nucleic Acids Res..

[16]  Jessica C Kissinger,et al.  Gene transfer in the evolution of parasite nucleotide biosynthesis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Ping Xu,et al.  Complete Genome Sequence of the Apicomplexan, Cryptosporidium parvum , 2004, Science.

[18]  Dinanath Sulakhe,et al.  PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways , 2005, Nucleic Acids Res..

[19]  Thomas A. Richards,et al.  Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements , 2006, Eukaryotic Cell.

[20]  I. Sherman,et al.  Isolation, characterization and synthesis of DNA from a malaria parasite. , 1968, The Journal of protozoology.

[21]  Andrei N Lupas,et al.  PhyloGenie: automated phylome generation and analysis. , 2004, Nucleic acids research.

[22]  Li Li,et al.  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data , 2003, Nucleic Acids Res..

[23]  David R Westhead,et al.  Annotating the Plasmodium genome and the enigma of the shikimate pathway. , 2004, Trends in parasitology.

[24]  Jessica C Kissinger,et al.  A first glimpse into the pattern and scale of gene transfer in Apicomplexa. , 2004, International journal for parasitology.

[25]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[26]  E. Koonin,et al.  Horizontal gene transfer in prokaryotes: quantification and classification. , 2001, Annual review of microbiology.

[27]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[28]  Eric M. Just,et al.  dictyBase, the model organism database for Dictyostelium discoideum , 2005, Nucleic Acids Res..

[29]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[30]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[31]  G. Petsko.  My worries are no longer behind me , 2007, Genome Biology.

[32]  Jessica C. Kissinger,et al.  TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi , 2005, Nucleic Acids Res..

[33]  J. Bull,et al.  An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis , 1993 .

[34]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[35]  Haiming Wang,et al.  ToxoDB: an integrated Toxoplasma gondii database resource , 2007, Nucleic Acids Res..

[36]  Sergio Verjovski-Almeida,et al.  Brazilian Symposium on Bioinformatics , 2007, Comput. Biol. Medicine.

[37]  Marek S. Skrzypek,et al.  Sequence resources at the Candida Genome Database , 2006, Nucleic Acids Res..

[38]  P. Rathod,et al.  Enzymes of purine and pyrimidine metabolism from the human malaria parasite, Plasmodium falciparum. , 1982, Molecular and biochemical parasitology.

[39]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[40]  Bindu Gajria,et al.  PlasmoDB: The Plasmodium Genome Resource , 2005 .

[41]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[42]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.