The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds

Suh, Alexander

doi:10.1007/s00239-015-9692-x

Cited by 31 publications

(34 citation statements)

References 27 publications

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“…CR1 LINEs, the most abundant group of TEs in crocodilians, and other TEs show an overall trend of decreased TE activity and diversity since the crocodilian ancestor. More precisely, crocodilian genomes exhibit a similar diversity of ancestral, amniote CR1 lineages as turtles (Suh 2015; Suh et al. 2015).…”

Section: Te Patterns In the Major Vertebrate Lineagesmentioning

confidence: 99%

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Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Sotero-Caio

Platt

Suh

et al. 2017

Genome Biology and Evolution

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237

227

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Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4–60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

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Section: Te Patterns In the Major Vertebrate Lineagesmentioning

confidence: 99%

“…2014). Notably, the diversity of CR1 in birds comprises 14 recognized families which emerged from a single CR1 lineage after the bird/crocodilian split, while the rest of the ancient amniote CR1 diversity was lost (Suh 2015; Suh et al. 2015).…”

Section: Te Patterns In the Major Vertebrate Lineagesmentioning

confidence: 99%

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Sotero-Caio

Platt

Suh

et al. 2017

Genome Biology and Evolution

Self Cite

237

227

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“…) . This CR1 dominance has been suggested to reflect the genome organization of the amniote ancestor and explains the scarcity of retro(pseudo)genes in the virtually L1‐lacking bird genomes . More precisely, most bird genomes contain only one ancient full‐length L1 copy or remnants thereof …”

Section: The Uniqueness Of Bird Genomesmentioning

confidence: 99%

“…CR1 is the dominant LINE superfamily of birds and is structurally very similar to L1 (dominant in therian mammals and virtually absent in birds (Fig. )), except for the presence of a hairpin and octamer microsatellite tail instead of an A‐rich tail . Structural elements are color coded, namely 5′ UTRs (blue), 3′ UTRs (red), LTRs (green), ORFs (gray), TIRs (purple), and tRNAs (yellow).…”

Section: The Diversity Of Avian Transposons and Endogenous Viral Elemmentioning

confidence: 99%

Evolution of bird genomes—a transposon's‐eye view

Kapusta

Suh

2016

Annals of the New York Academy of Sciences

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158

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Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

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“…If proteins encoded by non-LTR retroelements recognize a particular sequence of its own mRNA, as it seems to be the case for the CR1 element, this limits the types of cellular RNAs that can hitchhike and be retrotransposed (International Chicken Genome Sequencing 2004; Suh 2015). …”

Section: Mechanisms Of Retrocopy Formationmentioning

confidence: 99%

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

Casola

Betrán

2017

Genome Biology and Evolution

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Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene’s transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different “life cycle” stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.

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The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds

Cited by 31 publications

References 27 publications

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Evolution of bird genomes—a transposon's‐eye view

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

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