HTT-DB: Horizontally transferred transposable elements database

Dotto, Bruno Reis; Carvalho, Evelise Leis; Silva, Alexandre Freitas; Silva, Luiz Fernando Duarte; Pinto, Paulo Marcos; Ortiz, Mauro Freitas; Wallau, Gabriel Luz

doi:10.1093/bioinformatics/btv281

Cited by 53 publications

(56 citation statements)

References 12 publications

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“…2 and Dataset S2). This unprecedented figure is more than four times higher than the total number of HTT events reported so far in metazoans, plants, and fungi combined (10). Such a high number is still not unexpected, given that studies focusing on one or a few TEs often found one or more HTT events between multiple, distantly related taxa (11,(14)(15)(16)22).…”

Section: Significancementioning

confidence: 76%

“…In fact, most of the genetic material that is horizontally transferred in animals and plants consists of transposable elements (TEs) (9)(10)(11), which are pieces of DNA able to move from a chromosomal locus to another (12). The greater ability of TEs to move between organisms certainly relates to their intrinsic ability to transpose within genomes, which genes cannot do.…”

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confidence: 99%

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Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

200

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Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.horizontal transfer | transposable elements | insects | genome evolution | biogeography H orizontal transfer (HT) is the transmission of genetic material between organisms through a mechanism other than reproduction. In prokaryotes, HT is pervasive, its mechanisms are well understood, and it is now viewed as one of the main forces shaping genome architecture and evolution (1, 2). In contrast, the study of HT in eukaryotes is less documented, but has been increasingly investigated. The majority of genes horizontally acquired by eukaryotes come from bacteria, but the extent to which these transfers have contributed to eukaryote evolution is still unclear (3, 4). Gene transfers from eukaryote to eukaryote appear to be largely limited to filamentous organisms, such as oomycetes and fungi (5, 6).In animals and plants, very few cases of such horizontal gene transfers (HGTs) have been reported so far (7,8). In fact, most of the genetic material that is horizontally transferred in animals and plants consists of transposable elements (TEs) (9-11), which are pieces of DNA able to move from a chromosomal locus to another (12). The greater ability of TEs to move between organisms certainly relates to their intrinsic ability to transpose within genomes, which genes cannot do. HT of TEs (HTT) may allow these elements to enter naive genomes, which they invade by making copies of themselves, and then escape before they become fully silenced by anti-TE defenses (13). A growing number of studies have identified such HTT (11,[14][15][16]. However, a common drawback of these studies has been the inclusion of a limited set of TEs (11) or organisms (16), which hampers our understanding of the breadth of HTT, its contribution to genome evolution, and of the factors and barriers shaping these transfe...

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Section: Significancementioning

confidence: 76%

mentioning

confidence: 99%

Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

200

236

View full text Add to dashboard Cite

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“…The presence of such patterns can be explained by an exchange of TEs by these species or independent acquisitions from a third source, which characterizes a phenomenon known as HTT. HTT events have been reported throughout the eukaryote tree of life in recent years, and several of these events were reported for vertebrate species [13]. For instance, the SPIN transposon was found in more than 17 distantly related tetrapod species, including mammals as well as an African frog and a lizard, showing high similarity and patchy distribution [53,54].…”

Section: Discussionmentioning

confidence: 99%

“…However, compelling evidence in a wide variety of taxa has increasingly revealed that Horizontal Transfer (HT), the exchange of genetic material between isolated sexual species, is an effective way in which TEs invade new genomes and colonize other species [11,12]. Currently, around 2853 Horizontal Transposon Transfer (HTT) events have been reported [13]. The mariner family of Class II DNA transposons has the highest number of HTT cases reported (52) [13,14].…”

Section: Introductionmentioning

confidence: 99%

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Evolutionary history of the mariner element galluhop in avian genomes

et al. 2017

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Background: Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses. Results: galluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros). The copy number ranged from 5 to 10,158, in the genomes of C. japonica and G. gallus respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the G. gallus and M. gallopavo genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that galluhop homolog sequences form a new mariner subfamily, which we termed Gallus. Inter-species and intragenomic galluhop distance analyses indicated a high identity between the consensus of B. rhinoceros and the other 5 related species, and different emergence ages of the element between the Galliformes species and B. rhinocerus, suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species.Conclusions: Overall, our results showed that mariner elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of G. gallus and M. gallopavo. In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new mariner family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a galluhop element occurred between Galliformes and Buceritiformes.

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Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects

2017

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Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon.

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HTT-DB: Horizontally transferred transposable elements database

Abstract: bdotto82@gmail.com or gabriel.wallau@gmail.com.

Cited by 53 publications

References 12 publications

Massive horizontal transfer of transposable elements in insects

Massive horizontal transfer of transposable elements in insects

Evolutionary history of the mariner element galluhop in avian genomes

Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects

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