Rex Retroelements and Teleost Genomes: An Overview

Carducci, Federica; Barucca, Marco; Canapa, Adriana; Biscotti, Maria Assunta

doi:10.3390/ijms19113653

Cited by 24 publications

(25 citation statements)

References 66 publications

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“…HTT is prolific and particularly well described in aquatic microbial communities (reviewed in-depth in Sobecky and Hazen, 2009 (29) ). HTT of LINEs, LTR retrotransposons and DNA transposons has been reported in marine metazoans, with past studies describing the transfer of Rex1s and Rex3s between teleost fishes (9,30) ,…”

Section: Discussionmentioning

confidence: 99%

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

Galbraith

Ludington

Suh

et al. 2020

Preprint

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While numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Mya. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. Such major shifts in habitat should require significant genomic changes.The six subfamilies of LINE retrotransposons identified in the olive sea snake ( Aipysurus laevis ) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all six were absent from other amniotes, including terrestrial elapids, with the most similar transposons present in fish and marine invertebrates. The one exception was a similar transposon found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment following their divergence from terrestrial species 25 Mya. Our finding of repeated horizontal transfer events into separate lineages of marine snakes greatly expands past findings of frequent horizontal transfer in the marine environment, suggesting it is ideal for the transfer of transposons.Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. This provides evidence of the environment influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material. Significance StatementRecent research has found horizontal transfer (HT) of transposons between marine animals. We analyzed the olive sea snake ( Aipysurus laevis ) genome, uncovering HT of six novel retrotransposons into sea snakes since their marine transition within the last 18 Mya. All six are absent from terrestrial animals and are most similar to retrotransposons found in fish, corals and the independently marine sea kraits. All six retrotransposons are likely still active and expanding across the genome in A. laevis . Our findings suggest the marine environment is ideal for the HT of transposons; and provide evidence that changing environments can influence evolution not only through novel selective pressures, but also by contributing novel genomic material. Main Text

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Section: Discussionmentioning

confidence: 99%

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

Galbraith

Ludington

Suh

et al. 2020

Preprint

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“…This dynamic character causes TEs to have a major influence on the composition and evolution of the genome of animals and plants. According to their mechanism of transposition, the TEs are classified as retrotransposons (Class I -transposition occur via an RNA intermediate) or DNA transposons (Class II -transposition occur via DNA) (Biscotti et al, 2015;Carducci et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…The class of retrotransposons includes long terminal repeat (LTR) retrotransposons and non-LTR retrotransposons (Biscotti et al, 2015;Carducci et al, 2018). According to Volff et al (1999Volff et al ( , 2001Volff et al ( , 2002, the retroelements Rex1, Rex3 and Rex6 are abundant in the teleost genomes.…”

Section: Introductionmentioning

confidence: 99%

“…Despite Rex1, Rex3 and Rex6 are usually analyzed together, they have differences in structural organization (Carducci et al, 2018). Rex1 comprises apurinic/ apyrimidinic endonuclease sequences located upstream (or downstream) of the reverse transcriptase domain, a conserved 3'-untranslated region followed by an oligonucleotide sequence (Volff et al, 2000;Carducci et al, 2018). Rex3 is characterized by domains of reverse transcriptase, absence of LTR flanking regions, a 3'-end that comprises two repeats of GAA and tandem repeats of GATC, and the stop codon that are located at 3 nucleotides upstream of the first GAA repeat.…”

Section: Introductionmentioning

confidence: 99%

“…Rex3 is characterized by domains of reverse transcriptase, absence of LTR flanking regions, a 3'-end that comprises two repeats of GAA and tandem repeats of GATC, and the stop codon that are located at 3 nucleotides upstream of the first GAA repeat. Rex6 consists of a reverse transcriptase and a putative restriction enzyme-like endonuclease (Carducci et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)

et al. 2019

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The transposable elements (TE) have been widely applied as physical chromosome markers. However, in Loricariidae there are few physical mapping analyses of these elements. Considering the importance of transposable elements for chromosomal evolution and genome organization, this study conducted the physical chromosome mapping of retroelements (RTEs) Rex1, Rex3 and Rex6 in seven species of the genus Harttia and four species of the genus Hypostomus, aiming to better understand the organization and dynamics of genomes of Loricariidae species. The results showed an intense accumulation of RTEs Rex1, Rex3 and Rex6 and dispersed distribution in heterochromatic and euchromatic regions in the genomes of the species studied here. The presence of retroelements in some chromosomal regions suggests their participation in various chromosomal rearrangements. In addition, the intense accumulation of three retroelements in all species of Harttia and Hypostomus, especially in euchromatic regions, can indicate the participation of these elements in the diversification and evolution of these species through the molecular domestication by genomes of hosts, with these sequences being a co-option for new functions.Os elementos transponíveis (TE) têm sido amplamente aplicados como marcadores cromossômicos. Contudo, em Loricariidae, há poucas análises de mapeamento físico destes elementos. Considerando a importância de elementos transponíveis para a evolução cromossômica e organização genômica, este trabalho realizou o mapeamento físico cromossômico dos retroelementos (RTEs) Rex1, Rex3 e Rex6 em sete espécies do gênero Harttia e em quatro espécies do gênero Hypostomus, com o intuito de melhor compreender a organização e dinâmica dos genomas das espécies de Loricariidae. Os resultados evidenciaram um intenso acúmulo dos RTEs Rex1, Rex3 e Rex6 e distribuição dispersa em regiões heterocromáticas e eucromáticas no genoma das espécies estudadas. A presença de retroelementos em algumas regiões cromossômicas sugere sua participação em vários rearranjos cromossômicos. Além disso, o intenso acúmulo dos três retroelementos em todas as espécies de Harttia e Hypostomus, especialmente em regiões eucromáticas, pode indicar a participação destes elementos na diversificação e evolução destas espécies através da domesticação molecular pelo genoma dos hospedeiros, com estas sequências sendo cooptadas paras novas funções.Palavras-chave: Cascudos, Elementos transponíveis, Hibridização in situ fluorescente, Hypostominae, Loricariinae.

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Vertebrate Genome Size and the Impact of Transposable Elements in Genome Evolution

Biscotti

Carducci

Olmo

et al. 2019

Evolution, Origin of Life, Concepts and Methods

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Rex Retroelements and Teleost Genomes: An Overview

Cited by 24 publications

References 66 publications

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

New environment, new invaders - repeated horizontal transfer of LINEs to sea snakes

Chromosomal distribution of the retroelements Rex 1, Rex 3 and Rex 6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)

Vertebrate Genome Size and the Impact of Transposable Elements in Genome Evolution

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