Orthology prediction methods: A quality assessment using curated protein families

Trachana, Kalliopi; Larsson, Tomas; Powell, Sean; Chen, Wei‐Hua; Doerks, Tobias; Muller, Jean; Bork, Peer

doi:10.1002/bies.201100062

Cited by 128 publications

(176 citation statements)

References 60 publications

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“…Although OrthoMCL performs reasonably well to predict OGs in different benchmark studies (25,26), it also has some drawbacks that can lead to misinterpretation of the data (27). In addition, the outcome might be susceptible to the choice of the inflation parameter, which controls the size of the OGs.…”

Section: Resultsmentioning

confidence: 99%

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Smet

Adams

Vandepoele

et al. 2013

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

342

373

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The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication

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Section: Resultsmentioning

confidence: 99%

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Smet

Adams

Vandepoele

et al. 2013

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

342

373

View full text Add to dashboard Cite

show abstract

“…Given this, the next step should be to accurately estimate orthology and paralogy relationships of all of the genes that experienced WGD. For the analysis of gene orthology and paralogy, a homology search-or synteny-based approach has usually been used (9). In addition to the homology search-based approach (e.g., COGs and OrthoDB), a phylogenetic tree-based approach has also been introduced (e.g., Ensembl and PhylomeDB) (9).…”

mentioning

confidence: 99%

“…For the analysis of gene orthology and paralogy, a homology search-or synteny-based approach has usually been used (9). In addition to the homology search-based approach (e.g., COGs and OrthoDB), a phylogenetic tree-based approach has also been introduced (e.g., Ensembl and PhylomeDB) (9). Recent developments of tree search algorithms and increased computing power allow a sophisticated tree-based approach, comparing each gene tree with the species tree.…”

mentioning

confidence: 99%

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

Inoue

Sato

Sinclair

et al. 2015

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

171

130

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Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post-teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70-80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.orthologous gene | bony vertebrates | post-WGD genome evolution T he recent rapid growth of genome data has made it possible to clarify major evolutionary events that have shaped eukaryote genomes, such as gene duplication, chromosomal rearrangement, and whole-genome duplication (WGD) (1). In particular, WGD events, known to have occurred in several major lineages of flowering plants (2), budding yeasts (3), and vertebrates (4) (Fig. 1A), are considered to have had a major impact on genomic architecture and consequently organismal features.Duplicate genes generated by WGD are typically assumed to be redundant and therefore subsequently lost in a stochastic manner. Comparative genome studies have suggested that 90% of duplicate genes were rapidly lost (5) by a neutral process (6) after WGD in budding yeast, but 20-30% of them were retained in human (7) even after several hundred million years. However, few genome-wide studies have addressed the temporal pattern of gene loss or persistence after WGD with reference to a reliable timescale (but see refs. 6 and 8). Such examination is indispensable for understanding when duplicate genes were lost and, consequently, genome structures were reshaped, during vertebrate diversification after the WGD (Fig. 1).To examine the detailed process of duplicate gene loss after WGD, one needs to estimate the number (proportion) of remaining duplicates in extant and ancestral species. For this purpose, both (i) reliably time-calibrat...

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“…With the fast-paced, and still accelerating, accumulation of genome sequences in the databases, automated approaches for genome analysis are essential to keep up with the data and provide the foundation for subsequent detailed evolutionary and functional studies. A well-established approach in comparative genomics involves construction of clusters of orthologous genes from large sets of diverse organisms (18)(19)(20). Computational methods have been developed to delineate clusters of likely orthologs from diverse organisms, and several collections of ortholog clusters have been constructed and have become indispensable tools for genome annotation and phylogenomics (21)(22)(23).…”

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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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Orthology prediction methods: A quality assessment using curated protein families

Cited by 128 publications

References 60 publications

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

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