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Functional Retrogenes in Animal Genomes

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Abstract

The discovery of retrogenes was one of the most surprising breakthroughs of human genomics and had a big impact on other species genomic analyses. Since that moment, retrosequences first considered as useless and unimportant biological elements have been started to be widely studied. Now we know that retrogenes may be functional and can play a crucial role in shaping genomes and transcriptomes, working as sources of new genes or regulatory elements. Here, we describe some insights from RNA-based duplication studies which are focused mainly on numbers of retrogenes in various animal species, methods of functional retrogenes identification, their evolution, and impact on developing interspecies differences.

Keywords

  • Ribosomal Protein Gene
  • Corneal Dystrophy
  • Retrotransposable Element
  • Inflammasome Formation
  • Shaping Genome

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Fig. 16.1

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Correspondence to Joanna Ciomborowska .

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Glossary

Retrogene

Expressed and functional retrocopy; product of multi-exon parental gene mRNA retroposition

Retrocopy

product of multi-exon parental gene mRNA retroposition

Retropseudogene

Non-functional retrocopy, usually with degenerative mutations and genetic defects which become silenced short after retroposition

Parental Gene

Multi-exon gene which gives birth to retrocopy, works as a source of mRNA during retroposition

Duplication

Appearance of gene copies which are heritable

Retroposition

A mechanism in which mRNA of parental gene is reversely transcribed and new retrocopy is incorporated in new genomic positions (also known as RNA-based duplication or retroduplication)

Homologs

Genes which have common origin

Paralogs

Homologous genes related because of duplication

Orthologs

Homologous genes originating from a single ancestral gene in the last common ancestor of the compared genomes, genes related through speciation

Subfunctionalization

Subdivision of function between retrocopy and parental gene as a result of accumulation of degenerative mutation in duplicate

Neofunctionalization

The development of new function in duplicated gene as a result of the accumulation of neutral mutations

MSCI

Meiotic sex chromosome inactivation-process in which genes related to sex development are transcriptionally silenced

Ka/Ks ratio

Ratio between two values-a (the rate of substitution at non-synonymous sites in nucleotide sequence) and Ks (the rate of substitution at synonymous sites). Ka/Ks is often used to deduce type of the selection. Ka/Ks < 1 functional constraint, Ka/Ks = 1 lack of functional constraint; Ka/Ks > 1 positive Darwinian selection.

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Ciomborowska, J., Kubiak, M., Makałowska, I. (2012). Functional Retrogenes in Animal Genomes. In: Pontarotti, P. (eds) Evolutionary Biology: Mechanisms and Trends. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30425-5_16

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