Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

Semple, Colin A.; Wolfe, Kenneth H.

doi:10.1007/pl00006498

Cited by 132 publications

(121 citation statements)

References 36 publications

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“…There also have been several reports of conserved synteny, but not gene order, between Caenorhabditis elegans and Drosophila melanogaster or mammals (35)(36)(37)(38). Small inversions have been observed directly in comparisons of C. elegans vs. C. briggsae (39) and of D. melanogaster vs. D. buzzatii (40) and have been suggested by a genomewide analysis of the organization of tandem gene arrays in C. elegans (41). For plants, analysis of duplicated regions in the Arabidopsis thaliana genome has revealed several inversions with sizes ranging from megabases (hundreds of genes) (42)(43)(44) down to single genes (44).…”

Section: Discussionmentioning

confidence: 99%

Prevalence of small inversions in yeast gene order evolution

Seoighe

Federspiel

Jones

et al. 2000

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

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137

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Gene order evolution in two eukaryotes was studied by comparing the Saccharomyces cerevisiae genome sequence to extensive new data from whole-genome shotgun and cosmid sequencing of Candida albicans. Gene order is substantially different between these two yeasts, with only 9% of gene pairs that are adjacent in one species being conserved as adjacent in the other. Inversion of small segments of DNA, less than 10 genes long, has been a major cause of rearrangement, which means that even where a pair of genes has been conserved as adjacent, the transcriptional orientations of the two genes relative to one another are often different. We estimate that about 1,100 single-gene inversions have occurred since the divergence between these species. Other genes that are adjacent in one species are in the same neighborhood in the other, but their precise arrangement has been disrupted, probably by multiple successive multigene inversions. We estimate that gene adjacencies have been broken as frequently by local rearrangements as by chromosomal translocations or long-distance transpositions. A bias toward small inversions has been suggested by other studies on animals and plants and may be general among eukaryotes.

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Section: Discussionmentioning

confidence: 99%

Prevalence of small inversions in yeast gene order evolution

Seoighe

Federspiel

Jones

et al. 2000

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

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137

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“…Clear examples of gene conversion are documented in plants, fungi and animals (for example, see Semple and Wolfe, 1999;Drouin, 2002;Rozen et al, 2003;MondragonPalomino and Gaut, 2005). It has also been shown that gene conversion can principally be active after WGD by studies in yeast (Wolfe and Shields, 1997;Kellis et al, 2004).…”

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Whole-genome duplication in teleost fishes and its evolutionary consequences

2014

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Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change. AbstractWhole genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, the by far most species-rich vertebrate clade. After initial controversy, evidence is now solid that such an event took place in the common ancestor of all extant teleosts, the so-called teleostspecific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both copies of the gene. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosageselection (preserving genes to maintain dosage-balance between interconnected components).Since the frequency of these mechanisms is influenced by the gene's properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massi...

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“…However, Wolfe and Shields (1997) provided no evidence that the putative duplicated blocks in the yeast genome did in fact duplicate simultaneously as expected under the polyploidization hypothesis. Similar analyses have not been conducted for other genomes, aside from that of Semple and Wolfe (1999) applied to a set consisting of about 45% of the protein-coding genes of Caenorhabditis elegans.…”

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Gene Duplication and the Structure of Eukaryotic Genomes

Friedman

Hughes²

2001

Genome Res.

156

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A simple method for understanding how gene duplication has contributed to genomic structure was applied to the complete genomes of Caenorhabditis elegans, Drosophila melanogaster, and yeast Saccharomyces cerevisiae. By this method, the genes belonging to gene families (the paranome) were identified, and the extent of sharing of two or more families between genomic windows was compared with that expected under a null model. The results showed significant evidence of duplication of genomic blocks in both C. elegans and yeast. In C. elegans, the five block duplications identified all occurred intra-chromosomally, and all but one occurred quite recently. In yeast, by contrast, 39 duplicated blocks were identified, and all but one of these was inter-chromosomal. Of these 39 blocks, 28 showed evidence of ancient duplication, possibly as a result of an ancient polyploidization event. By contrast, three blocks showed evidence of very recent duplication, while seven others showed a mixture of ancient and recent duplication events. Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200-300 million years.

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Gene Duplication and Gene Conversion in the Caenorhabditis elegans Genome

Cited by 132 publications

References 36 publications

Prevalence of small inversions in yeast gene order evolution

Prevalence of small inversions in yeast gene order evolution

Whole-genome duplication in teleost fishes and its evolutionary consequences

Gene Duplication and the Structure of Eukaryotic Genomes

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