Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish &lt;i&gt;Tetraodon nigroviridis&lt;/i&gt;

Fischer, Cécile; Bouneau, Laurence; Coutanceau, Jean-Pierre; Weissenbach, Jean; Ozouf−Costaz, Catherine; Volff, Jean Nicolas

doi:10.1159/000084985

Cited by 11 publications

(7 citation statements)

References 171 publications

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“…In the current study, we found that teleost fish genomes represent extremely high diversity of TEs compared with the other vertebrate genomes, which is in agreement with the previous studies [ 18 , 21 , 22 , 40 ]; furthermore, we performed a systematic comparative analysis of the intra-lineage diversity and activity of TEs across the four teleosts, and our data suggested that the differences in genome content among taxa are not limited to differences in a specific type of TE accumulation. The differences in both the diversity and activity of TEs contribute to the variances of TEs across teleost lineages.…”

Section: Discussionsupporting

confidence: 93%

The contribution of transposable elements to size variations between four teleost genomes

et al. 2016

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BackgroundTeleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained.ResultsIn this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome.ConclusionOverall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 93%

The contribution of transposable elements to size variations between four teleost genomes

et al. 2016

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“…Even the very compact genomes of the smooth pufferfishes with their low repeat content show a higher diversity of endogenous retroelements than mammalian genomes: 22 and 15 families were detected in Fugu and Tetraodon, respectively. A similar situation is observed for DNA transposons [92,99]. On the other hand, endogenous retroviruses, which were introduced independently through infection into the different vertebrate lineages, are present in both teleost fishes and tetrapods, as well as non-coding retroelements called SINEs (short interspersed nuclear elements, for example Alu sequences in humans).…”

Section: Differential Evolution Of Transposable Elements In Fish and mentioning

confidence: 57%

Fish Genomes, Comparative Genomics and Vertebrate Evolution

Froschauer

Braasch

Volff

2006

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Genome sequences from the pufferfishes Takifugu rubripes (Fugu) and Tetraodon nigroviridis, the zebrafish Danio rerio and the medaka Oryzias latipes together with genomic data from various other fish species have opened an important era of comparative genomics shedding a new light on the structure and evolution of vertebrate genomes. For instance, comparative analysis of fish genomes has revealed that the ancestral bony vertebrate genome was composed of 12 chromosomes, has confirmed the occurrence of at least one event of genome duplication in the early history of vertebrates and has allowed the identification of conserved regulatory and coding sequences in the human genome. Importantly, major differences have been observed between teleost fish and mammalian genomes. There is now convincing evidence that all teleosts are derived from a common tetraploid fish ancestor. This tetraploidization event arose about 320-350 million years ago in the ray-finned fish lineage, followed by rediploidization and retention of hundreds of duplicate pairs. Divergent evolution of the resulting duplicates has been proposed to be involved in the species richness observed in teleost fishes. Fish genomes also contain many more families of transposable elements than mammals and birds. Finally, while the mammalian and bird lineages possess major sex determination systems with sex chromosomes conserved in very divergent species, fishes have very frequently switched between sex determination mechanisms and repeatedly created novel sex chromosomes during evolution. Hence, teleost fishes display a high level of genomic plasticity, which might be related to the astonishing biodiversity observed in these animals.

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“…Within actinopterygians, differences were even observed between related fish species: The genome of the platyfish contains many more old TE copies than that of the related medaka. Differences in TE elimination between fish species might be supported by the genome architecture of the pufferfish: In this compact and TE-poor genome, all types of repeats are excluded from euchromatic gene-rich regions and accumulate in particular heterochromatic compartments, a structure generally not observed in other fish species ( Dasilva et al 2002 ; Fischer et al 2005 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

Chalopin

Naville

Plard

et al. 2015

Genome Biology and Evolution

328

397

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Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.

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Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish <i>Tetraodon nigroviridis</i>

Cited by 11 publications

References 171 publications

The contribution of transposable elements to size variations between four teleost genomes

The contribution of transposable elements to size variations between four teleost genomes

Fish Genomes, Comparative Genomics and Vertebrate Evolution

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

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