Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in <i>E. coli</i>

Daubin, Vincent; Ochman, Howard

doi:10.1101/gr.2231904

Cited by 244 publications

(287 citation statements)

References 44 publications

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“…The majority with significant BLAST (61) hits match genomes of closely related Sulfolobales species or their mobile elements (Table S3), suggesting that horizontal gene transfer from divergent species is a rare event. As in other analyses of microbial species (40,45,59,60,63), many of the gained genes in S. islandicus have no significant BLAST match to the public databases (Table S3).…”

Section: Biogeography Of the Variable Genomementioning

confidence: 99%

Biogeography of theSulfolobus islandicuspan-genome

Reno¹,

Held²,

Fields

et al. 2009

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

225

242

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Variation in gene content has been hypothesized to be the primary mode of adaptive evolution in microorganisms; however, very little is known about the spatial and temporal distribution of variable genes. Through population-scale comparative genomics of 7 Sulfolobus islandicus genomes from 3 locations, we demonstrate the biogeographical structure of the pan-genome of this species, with no evidence of gene flow between geographically isolated populations. The evolutionary independence of each population allowed us to assess genome dynamics over very recent evolutionary time, beginning ≈910,000 years ago. On this time scale, genome variation largely consists of recent strain-specific integration of mobile elements. Localized sectors of parallel gene loss are identified; however, the balance between the gain and loss of genetic material suggests that S. islandicus genomes acquire material slowly over time, primarily from closely related Sulfolobus species. Examination of the genome dynamics through population genomics in S. islandicus exposes the process of allopatric speciation in thermophilic Archaea and brings us closer to a generalized framework for understanding microbial genome evolution in a spatial context.

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Section: Biogeography Of the Variable Genomementioning

confidence: 99%

Biogeography of theSulfolobus islandicuspan-genome

Reno¹,

Held²,

Fields

et al. 2009

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

225

242

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“…Support for this hypothesis has been given by the studies of Domazet-Loso and Tautz (2003) and Daubin and Ochman (2004), in Drosophila and bacteria, respectively. In the present study, this hypothesis has been further tested with respect to the Ascomycotan fungi.…”

Section: Discussionmentioning

confidence: 90%

“…A proposed explanation of this problem has been that some genes evolve so rapidly that their homologues cannot be discovered over larger evolutionary distances (Schmid and Aquadro 2001). Although this has been supported by recent findings in Drosophila and bacteria that orphan genes evolve, on average, more than three times faster than nonorphan genes (Daubin and Ochman 2004;Domazet-Loso and Tautz 2003), the influence of other factors on the evolutionary rate of genes should be taken into account. These factors include the expression level of genes (Hastings 1996;Pal et al 2001), a gene's dispensability (the organism's fitness after deletion of the gene) (Hirsh and Fraser 2001;Krylov et al 2003), gene essentiality (Wilson et al 1977), gene duplication (Jordan et al 2002b;Yang et al 2003), and the number of protein-protein interactions involving the gene's product (Fraser et al 2003;Wagner 2001).…”

Section: Introductionmentioning

confidence: 93%

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

et al. 2006

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Abstract. The evolutionary origin of ''orphan'' genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineagespecific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.

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“…As described above, DNA of lateral origin has passed filters that can skew its composition. In most g-proteobacteria, ORFans (genes without significant matches in current databases) are AþT-rich, suggesting a phage ancestry Daubin & Ochman 2004). Successive LGT events can superimpose DNA onto previously incorporated regions, resulting in a genomic pastiche that may defy analysis; Chan et al (2009) found that 5.5 per cent of 1462 orthologue families exhibit complex recombination patterns consistent with successive layering of LGT.…”

Section: Quantificationmentioning

confidence: 99%

“…The relative contribution of each LGT process is not well understood, but in many cases the processes leave tell-tale clues (Zaneveld et al 2008). ORFans in bacteria are often enriched in A þ T compared with the rest of the genome, suggesting residence in bacteriophage (Daubin & Ochman 2004). Genes on plasmids often show divergent nucleotide composition (Nakamura et al 2004) and phylogenetic relationships (Gerdes et al 2000) indicative of xenologous origin.…”

Section: (B)mentioning

confidence: 99%

Lateral genetic transfer: open issues

Ragan

Beiko

2009

Phil. Trans. R. Soc. B

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Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.

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Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli

Cited by 244 publications

References 44 publications

Biogeography of theSulfolobus islandicuspan-genome

Biogeography of theSulfolobus islandicuspan-genome

Accelerated Evolutionary Rate May Be Responsible for the Emergence of Lineage-Specific Genes in Ascomycota

Lateral genetic transfer: open issues

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