About: Degeneracy and genetic assimilation in RNA evolution

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Degeneracy and genetic assimilation in RNA evolution
Creator	Reidys, Christian Rezazadegan, Reza
Source	PMC
abstract	BACKGROUND: The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The relation between neutrality and adaptation has been studied in the context of RNA before and here we further study transitional mutations in the context of degenerate (plastic) RNA sequences and genetic assimilation. We propose quasineutral mutations, i.e. mutations which preserve an element of the phenotype set, as minimal mutations and study their properties. We also propose a general probabilistic interpretation of genetic assimilation and specialize it to the Boltzmann ensemble of RNA sequences. RESULTS: We show that degenerate sequences i.e. sequences with more than one structure at the MFE level have the highest evolvability among all sequences and are central to evolutionary innovation. Degenerate sequences also tend to cluster together in the sequence space. The selective pressure in an evolutionary simulation causes the population to move towards regions with more degenerate sequences, i.e. regions at the intersection of different neutral networks, and this causes the number of such sequences to increase well beyond the average percentage of degenerate sequences in the sequence space. We also observe that evolution by quasineutral mutations tends to conserve the number of base pairs in structures and thereby maintains structural integrity even in the presence of pressure to the contrary. CONCLUSIONS: We conclude that degenerate RNA sequences play a major role in evolutionary adaptation.
has issue date	2018-12-27(xsd:dateTime)
bibo:doi	10.1186/s12859-018-2497-3
bibo:pmid	30587112
has license	cc-by
sha1sum (hex)	444cc65fbe22dd6583120260c488dd621ebadab4
schema:url	https://doi.org/10.1186/s12859-018-2497-3
resource representing a document's title	Degeneracy and genetic assimilation in RNA evolution
has PubMed Central identifier	PMC6307299
has PubMed identifier	30587112
schema:publication	BMC Bioinformatics
resource representing a document's body	covid:444cc65fbe22dd6583120260c488dd621ebadab4#body_text
is schema:about of	named entity 'level' named entity 'leads' named entity 'driven' named entity 'minimal' named entity 'population' named entity 'mutations' named entity 'mutations' named entity 'observe' named entity 'HERE' named entity 'SPECIALIZE' named entity 'AVERAGE' named entity 'RNA SEQUENCES' named entity 'NON-' named entity 'A MAJOR' named entity 'TEND' named entity 'SEQUENCES' named entity 'ADAPTIVE' named entity 'INNOVATION' named entity 'PERCENTAGE' named entity 'DEGENERATE' named entity 'preserve' named entity 'mutations' named entity 'RNA' named entity 'studied' named entity 'sequence space' named entity 'innovation' named entity 'neutral' named entity 'Results' named entity 'mutations' named entity 'genetic assimilation' named entity 'sequence space' named entity 'neutral mutations' named entity 'RNA' named entity 'evolutionary adaptation' named entity 'genetic assimilation' named entity 'evolution' named entity 'mutation' named entity 'minuscule' named entity 'genotypic' named entity 'fitnesses' named entity 'mutation' named entity 'fitness functions' named entity 'neutral networks' named entity 'MFE' named entity 'deletions' named entity 'Phenotypic plasticity' named entity 'neutral networks' named entity 'genotype' named entity 'neutral network' named entity 'target structure' named entity 'MFE' named entity 'MFE' named entity 'quasineutral' named entity 'genotype' named entity 'RNA' named entity 'MFE' named entity 'phenotypes' named entity '3.8' named entity 'wild type' named entity 'RNA' named entity 'genetic assimilation' named entity 'degeneracy' named entity 'selective pressure' named entity 'neutral networks' named entity 'point mutants' named entity 'point mutations' named entity 'neutral mutations' named entity 'RNA' named entity 'quasineutral' named entity 'point mutants' named entity 'quasineutral' named entity 'quasineutral' named entity 'evolvability' named entity 'sequence space' named entity 'evolvability' named entity 'structure space' named entity 'sequence space' named entity 'quasineutral' named entity 'quasineutral' named entity 'leader RNA'

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