A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

Kristensen, David M.; Kannan, Lavanya; Coleman, Michael K.; Wolf, Yuri I.; Sorokin, Alexander V.; Koonin, Eugene V.; Mushegian, Arcady

doi:10.1093/bioinformatics/btq229

Cited by 197 publications

(176 citation statements)

References 41 publications

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“…Aside from the increase in the number and size of ATGCs due to the inclusion of new genomes of bacteria and archaea, the major difference between this and previous ATGC versions was the exclusion of lower-quality drafts of incomplete genomes. In addition, the pangenome of each ATGC is now represented by automatically derived COGs [67,68,82].…”

Section: Methodsmentioning

confidence: 99%

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Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

et al. 2014

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Background: Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species.

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Section: Methodsmentioning

confidence: 99%

“…and protein coverage of 75% [82]. Second, proteins unassigned in the first stage were added to the cluster that they match best using the COGNITOR method [83], with the stringent threshold e-value 1 × 10 −20 and protein coverage of 75%.…”

Section: Methodsmentioning

confidence: 99%

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

et al. 2014

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“…For delineation of the core genes and pan-genomes, a database of all the predicted proteins from the whole faustovirus genome was created. Protein clusters were built using COG triangles (36) and OrthoMCL (37) clustering algorithms (38), and the core genes and pan-genome were defined using GET_HOMOLOGUES software (38) with the following parameters: 75% minimum coverage and 30% minimum identity for the pairwise sequence alignments, with 1eϪ05 as the maximum E value.…”

Section: Flow Cytometric Analyses (I) Detection Of Amoeba Lysis By Fmentioning

confidence: 99%

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Reteno

Benamar

Khalil

et al. 2015

J Virol

172

227

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Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of Ϸ200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes Ϸ3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCEBy using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is Ϸ3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database). G iant viruses were first described in 2003, with the discovery of Acanthamoeba polyphaga mimivirus (1, 2). They are protistassociated viruses that belong to a major monophyletic group of double-stranded DNA (dsDNA) viruses known as nucleocytoplasmic large DNA viruses (NCLDVs), and they have been classified under the proposed order Megavirales (3). Since the first description of Acanthamoeba polyphaga mimivirus, giant viruses have been isolated from other phagocytic protists, primarily Acanthamoeba spp. (4-6). Because these giant viruses are resistant to killing by phagocytic protists, we hypothesized that they may also reproduce in macrophages and might therefore infect humans. This proposition was validated experimentally by the isolation of mimivirus from atypical pneumonia patients and by the detection of marseilleviruses in blood donors and in human lymph nodes (7-9). Moreover, we and others identified sequences associated with giant viruses in metagenomes generated from human tissues, suggesting that giant viruses are a component of the human virome (10). Because the investigation of a virome typically starts with a filtration procedure that eliminates giant viruses (11), we developed a new culture approach that does not prevent the detection of these viruses.In the present study, we de...

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“…In previous work, we constructed Ͼ2,000 phage orthologous groups (POGs), including genes from Ͼ500 phage genomes (24)(25)(26). We found that despite the ability of phages to acquire genes from their bacterial hosts, at least half of these POGs consist of genes that were never or only very rarely observed in bacteria outside recently integrated prophages.…”

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confidence: 99%

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

et al. 2013

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Viruses are the most abundant biological entities on earth and encompass a vast amount of genetic diversity. The recent rapid increase in the number of sequenced viral genomes has created unprecedented opportunities for gaining new insight into the structure and evolution of the virosphere. Here, we present an update of the phage orthologous groups (POGs), a collection of 4,542 clusters of orthologous genes from bacteriophages that now also includes viruses infecting archaea and encompasses more than 1,000 distinct virus genomes. Analysis of this expanded data set shows that the number of POGs keeps growing without saturation and that a substantial majority of the POGs remain specific to viruses, lacking homologues in prokaryotic cells, outside known proviruses. Thus, the great majority of virus genes apparently remains to be discovered. A complementary observation is that numerous viral genomes remain poorly, if at all, covered by POGs. The genome coverage by POGs is expected to increase as more genomes are sequenced. Taxon-specific, single-copy signature genes that are not observed in prokaryotic genomes outside detected proviruses were identified for two-thirds of the 57 taxa (those with genomes available from at least 3 distinct viruses), with half of these present in all members of the respective taxon. These signatures can be used to specifically identify the presence and quantify the abundance of viruses from particular taxa in metagenomic samples and thus gain new insights into the ecology and evolution of viruses in relation to their hosts.

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A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches

Cited by 197 publications

References 41 publications

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

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