COmplete GENome Tracking (COGENT): a flexible data 
environment for computational genomics

Janssen, Paul; Enright, Anton J.; Audit, Benjamin; Cases, Ildefonso; Goldovsky, Leon; Harte, Nicola; Kunin, Victor; Ouzounis, Christos A.

doi:10.1093/bioinformatics/btg161

Cited by 39 publications

(41 citation statements)

References 3 publications

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“…An example of such drawing is shown in Figure 3, with real data from this study. The full tree is available in VRML format, including all species identifiers (Janssen et al 2003), as Supplemental material.…”

Section: Discussionmentioning

confidence: 99%

The net of life: Reconstructing the microbial phylogenetic network

Kunin¹,

Goldovsky²,

Darzentas³

et al. 2005

Genome Res.

231

175

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It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the “net of life.” We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as “vines,” and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.

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Section: Discussionmentioning

confidence: 99%

The net of life: Reconstructing the microbial phylogenetic network

Kunin¹,

Goldovsky²,

Darzentas³

et al. 2005

Genome Res.

231

175

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“…To produce a homology search that would be both sensitive and specific, we built a profile alignment of the amino acid sequence of a range of eukaryotic homologs for each yeast gene, then used PSI-BLAST (44) to search against a database of 197 eubacterial and 22 archaebacterial genome sequences. To build the profile alignments for PSI-BLAST, each protein-coding gene in the Saccharomyces cerevisiae genome sequence [downloaded from the Cogent database (45)] was compared with the protein-coding gene content of six other eukaryotic genomes (Caenorhabditis elegans, Arabidopsis thaliana, Schizosaccharomyces pombe, Neu- Values are listed by domain of best BLAST hit, showing means and 95% bootstrap percentile CIs for the mean of each parameter (calculated using the nonparametric bootstrap). P values are bootstrap probabilities for the mean of the statistic in archaebacterial homologs being less than or equal to the mean in eubacterial homologs, based on 10,000 replicates.…”

Section: Methodsmentioning

confidence: 99%

Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function

Cotton

McInerney

2010

Proc. Natl. Acad. Sci. U.S.A.

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The traditional tree of life shows eukaryotes as a distinct lineage of living things, but many studies have suggested that the first eukaryotic cells were chimeric, descended from both Eubacteria (through the mitochondrion) and Archaebacteria. Eukaryote nuclei thus contain genes of both eubacterial and archaebacterial origins, and these genes have different functions within eukaryotic cells. Here we report that archaebacterium-derived genes are significantly more likely to be essential to yeast viability, are more highly expressed, and are significantly more highly connected and more central in the yeast protein interaction network. These findings hold irrespective of whether the genes have an informational or operational function, so that many features of eukaryotic genes with prokaryotic homologs can be explained by their origin, rather than their function. Taken together, our results show that genes of archaebacterial origin are in some senses more important to yeast metabolism than genes of eubacterial origin. This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome.endosymbiosis | gene essentiality | eukaryote origin | protein interaction network A s one of the three domains of cellular life, the eukaryotes are typically described as the sister group to the archaebacteria. This sister group relationship describes the evolutionary history of the "nuclear-cytoplasmic" component of eukaryotes, with mitochondria and plastids being of endosymbiotic bacterial origin (e.g., ref. 1). In this traditional scenario, the unique features of extant eukaryotes were gradually acquired in the eukaryote stem group before the endosymbiotic acquisition of the mitochondrion. Thus, the acquisition of the mitochondrion was an important, but not foundational, step in eukaryote origins, occurring subsequent to the evolution of many characteristic features of eukaryotic cell biology. Early molecular phylogenies of ribosomal RNA genes support this scenario (see refs. 2 and 3 for reviews), as do several other molecular markers. Many nuclear genes are more closely related to eubacterial homologs than to any known archaebacterial sequence (4, 5) and appear to have been transferred to the nucleus from the ancestral mitochondrial genome by a process known as endosymbiotic gene transfer (1, 6). A similar process occurred after other symbiotic events, for example, the introduction of many chloroplast-derived genes into the nuclei of green plants (6).An alternative view of eukaryotic nuclear-cytoplasmic origins, first suggested by Lake (7-9) is that this lineage arose from within, rather than as a sister to, the archaebacteria. This view is supported by molecular phylogenies showing that many eukaryote genes actually derive from within the archaebacterial domain (7-11), including a recent reanalysis of informational genes with modern phylogenetic methods (10). It also has become clear that those eukaryotes that lack mitochondria either are derived from organisms that have mitochondria or themse...

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“…BLAST searches (Altschul et al 1997) were used to compare the apicomplexan sequences with UniProt (version 9.0-3,554,507 sequences) (Apweiler et al 2004), COGENT (Feb 2007-915,554 sequences) (Janssen et al 2003), andPartiGeneDB (Feb 2007-2,174,649 sequences) (Peregrin-Alvarez et al 2005). For the BLAST programs (v2.2.13) used, see Supplemental Table S6.…”

Section: Taxonomic Profilesmentioning

confidence: 99%

The origins of apicomplexan sequence innovation

Wasmuth¹,

Daub²,

Peregrín-Alvarez³

et al. 2009

Genome Res.

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The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.

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COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics

Abstract: http://maine.ebi.ac.uk:8000/services/cogent/

Cited by 39 publications

References 3 publications

The net of life: Reconstructing the microbial phylogenetic network

The net of life: Reconstructing the microbial phylogenetic network

Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function

The origins of apicomplexan sequence innovation

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