Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication

Guo, Baocheng; Zou, Ming; Wagner, Andreas

doi:10.1093/molbev/mss108

Cited by 36 publications

(39 citation statements)

References 104 publications

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“…They have a lower percentage of repeated sequences (especially DNA transposons) and shorter intronic sequences. This situation would depend both on a high rate of intron and transposon loss and on a higher level of indels (insertions/ deletions) [Imai et al, 2007;Loh et al, 2008;Noleto et al, 2009;Guo et al, 2012].…”

Section: Deuterostomesmentioning

confidence: 99%

Transposons, Genome Size, and Evolutionary Insights in Animals

Canapa¹,

Barucca

Biscotti³

et al. 2015

Cytogenet Genome Res

126

104

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The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.

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Section: Deuterostomesmentioning

confidence: 99%

Transposons, Genome Size, and Evolutionary Insights in Animals

Canapa¹,

Barucca

Biscotti³

et al. 2015

Cytogenet Genome Res

126

104

View full text Add to dashboard Cite

show abstract

“…Both members of a paralogous gene pair have experienced significantly more insertion and deletion events than genes not retained as duplicates. These indels mostly occurred shortly after the duplication event and are predicted to affect protein structure more than amino acid substitutions (Guo et al, 2012).…”

mentioning

confidence: 99%

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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“…10 By contrast, the fundamental properties governing protein tolerance to indel events 11 are comparatively understudied. Previous efforts in comparative sequence analysis have 12 suggested that indels preferentially occur in disordered and/or loop regions and are less 13 common in regions with secondary structure [11][12][13][14][15]. Furthermore, indel events may be 14 more likely to occur on the protein surface, where residues are more exposed to solvent, 15 rather than in a protein's core [13,14].…”

mentioning

confidence: 99%

“…Previous efforts in comparative sequence analysis have 12 suggested that indels preferentially occur in disordered and/or loop regions and are less 13 common in regions with secondary structure [11][12][13][14][15]. Furthermore, indel events may be 14 more likely to occur on the protein surface, where residues are more exposed to solvent, 15 rather than in a protein's core [13,14]. Thus, constraints on indel events appear to 16 mirror those on substitution events, in that amino-acid substitutions are most frequent 17 in unstructured regions and on the protein surface [1].…”

mentioning

confidence: 99%

Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein

Jackson

Spielman

Wilke

2016

Preprint

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Proteins evolve through two primary mechanisms: substitution, where mutations alter a protein's amino-acid sequence, and insertions and deletions (indels), where amino acids are either added to or removed from the sequence. Protein structure has been shown to influence the rate at which substitutions accumulate across sites in proteins, but whether structure similarly constrains the occurrence of indels has not been rigorously studied. Here, we investigate the extent to which structural properties known to covary with protein evolutionary rates might also predict protein tolerance to indels. Specifically, we analyze a publicly available dataset of single-amino-acid deletion mutations in enhanced green fluorescent protein (eGFP) to assess how well the functional effect of deletions can be predicted from protein structure. We find that weighted contact number (WCN), which measures how densely packed a residue is within the protein's three-dimensional structure, provides the best single predictor for whether eGFP will tolerate a given deletion. We additionally find that using protein design to explicitly model deletions results in improved predictions of functional status when combined with other structural predictors. Our work suggests that structure plays fundamental role in constraining deletions at sites in proteins, and further that similar biophysical constraints influence both substitutions and deletions. This study therefore provides a solid foundation for future work to examine how protein structure influences tolerance of more complex indel events, such as insertions or large deletions.

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Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication

Cited by 36 publications

References 104 publications

Transposons, Genome Size, and Evolutionary Insights in Animals

Transposons, Genome Size, and Evolutionary Insights in Animals

Whole-genome duplication in teleost fishes and its evolutionary consequences

Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein

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