Genomic and Population-Level Effects of Gene Conversion in Caenorhabditis Paralogs

Katju, Vaishali; Bergthorsson, Ulfar

doi:10.3390/genes1030452

Cited by 11 publications

(12 citation statements)

References 69 publications

(102 reference statements)

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“…S2 and S3). These differences could be explained by a higher similarity of SWS2A copies because of the additional duplication event in percomorphs, which is likely to increase the chances and extent of gene conversion (23).…”

Section: Resultsmentioning

confidence: 99%

“…However, neofunctionalization can also include differential expression of genes throughout ontogeny (20). Finally, opsin duplicates might be subject to gene conversion (18,21), a common form of reticulate evolution that serves as an important homogenizing force or a repair mechanism between paralogous genes (23). Gene conversion typically occurs between functional paralogs, but it may also involve pseudogenized genes, thus leading to their resurrection (24).…”

Section: Significancementioning

confidence: 99%

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Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Cortesi

Musilová

Stieb

et al. 2014

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

143

212

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Single-gene and whole-genome duplications are important evolutionary mechanisms that contribute to biological diversification by launching new genetic raw material. For example, the evolution of animal vision is tightly linked to the expansion of the opsin gene family encoding light-absorbing visual pigments. In teleost fishes, the most species-rich vertebrate group, opsins are particularly diverse and key to the successful colonization of habitats ranging from the bioluminescence-biased but basically dark deep sea to clear mountain streams. In this study, we report a previously unnoticed duplication of the violet-blue short wavelength-sensitive 2 (SWS2) opsin, which coincides with the radiation of highly diverse percomorph fishes, permitting us to reinterpret the evolution of this gene family. The inspection of close to 100 fish genomes revealed that, triggered by frequent gene conversion between duplicates, the evolutionary history of SWS2 is rather complex and difficult to predict. Coincidentally, we also report potential cases of gene resurrection in vertebrate opsins, whereby pseudogenized genes were found to convert with their functional paralogs. We then identify multiple novel amino acid substitutions that are likely to have contributed to the adaptive differentiation between SWS2 copies. Finally, using the dusky dottyback Pseudochromis fuscus, we show that the newly discovered SWS2A duplicates can contribute to visual adaptation in two ways: by gaining sensitivities to different wavelengths of light and by being differentially expressed between ontogenetic stages. Thus, our study highlights the importance of comparative approaches in gaining a comprehensive view of the dynamics underlying gene family evolution and ultimately, animal diversification.

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Section: Resultsmentioning

confidence: 99%

Section: Significancementioning

confidence: 99%

Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Cortesi

Musilová

Stieb

et al. 2014

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

143

212

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“…A compelling direction for further exploration would leverage these data from X. victorianus to standardize diversity values from a natural population of X. laevis from Western Cape Province, South Africa, which is the probable source of many laboratory strains from which X. laevis sequence databases were generated. Another concern not addressed here is the possibility that gene conversion occurs between homeologs, and that this could lead to misinterpretations about their divergence, duplicate versus singleton status and other evolutionary characteristics [Katju and Bergthorsson, 2010]. Future work will also shed light on the possibility that more than one tetraploidization event generated extant Xenopus tetraploids with 36 chromosomes [Bewick et al, 2011], a scenario that would potentially have consequences for the duration of tetraploid ancestry prior to the speciation of X. laevis and X. victorianus .…”

Section: Molecular Polymorphism On Putative Singletons and Duplicatesmentioning

confidence: 99%

Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs <b><i>(Xenopus)</i></b>

Evans

Kwon

2015

Cytogenet Genome Res

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Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.

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“…Given that the duplicates in this study are thought to be of recent evolutionary origin based on their low K S values, this result demonstrates that paralogs start exhibiting the molecular signature of asymmetric evolution remarkably early in their evolutionary existence. Although gene conversion cannot be ruled out as a contributing factor to low synonymous divergence between paralogs and may serve to homogenize at least a fraction of the duplicate pairs within this dataset [51,52], it can at best only delay the inevitable sequence asymmetry in the molecular evolution of paralogs. Over longer evolutionary periods, this evident signature of divergent molecular evolution in the early life of paralogs may come to be obscured by later mutational events [24,47].…”

Section: Discussionmentioning

confidence: 99%

To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs

Katju

2013

BMC Evol Biol

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BackgroundGene duplicates often exhibit asymmetric rates of molecular evolution in their early evolutionary existence. This asymmetry in rates is thought to signify the maintenance of the ancestral function by one copy and the removal of functional constraint on the other copy, enabling it to embark on a novel evolutionary trajectory. Here I focused on a large population of evolutionarily young gene duplicates (KS ≤ 0.14) in the Caenorhabditis elegans genome in order to conduct the first combined analysis of four predictors (evolutionary age, chromosomal location, structural resemblance between duplicates, and duplication span) which may be implicated in the asymmetric sequence divergence of paralogs at the nucleotide and amino acid level. In addition, I investigate if either paralog is equally likely to embark on a trajectory of accelerated sequence evolution or whether the derived paralog is more likely to exhibit faster sequence evolution.ResultsThree predictors (evolutionary age of duplicates, chromosomal location and duplication span) serve as major determinants of sequence asymmetry between C. elegans paralogs. Paralogs diverge asymmetrically in sequence with increasing evolutionary age, the relocation of one copy to a different chromosome and attenuated duplication spans that likely fail to capture the entire ancestral repertoire of coding sequence and regulatory elements. Furthermore, for paralogs residing on the same chromosome, opposite transcriptional orientation and increased genomic distance do not increase sequence asymmetry between paralogs. For a subset of duplicate pairs wherein the ancestral versus derived paralog could be distinguished, the derived paralogs are more likely to evolve at accelerated rates.ConclusionsThis genome-wide study of evolutionarily young duplicates stemming primarily from DNA-mediated small-scale duplication events demonstrates that genomic relocation to a new chromosome has important consequences for asymmetric divergence of paralogs, akin to paralogs arising from RNA-mediated duplication events. Additionally, the duplication span is negatively correlated with sequence rate asymmetry among paralogs, suggesting that attenuated duplication spans stemming from incomplete duplication of the ORF and/or ancestral regulatory elements further accelerate sequence divergence between paralogs. Cumulatively, derived copies exhibit accelerated rates of sequence evolution suggesting that they are primed for a divergent evolutionary trajectory by changes in structure and genomic context at inception.

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Genomic and Population-Level Effects of Gene Conversion in Caenorhabditis Paralogs

Cited by 11 publications

References 69 publications

Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs <b><i>(Xenopus)</i></b>

To the beat of a different drum: determinants implicated in the asymmetric sequence divergence of Caenorhabditis elegans paralogs

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