Internal deletions of transposable elements: the case of Lemi elements

Evolutionary History of the DD41D Family of Tc1/Mariner Transposons in Two Mayetiola Species

Tc1/mariner elements are ubiquitous in eukaryotic genomes including insects. They are diverse and divided into families and sub-families. The DD34D family including mauritiana and irritans subfamilies have already been identified in two closely related species of Cecidomyiids M. destructor and M. hordei. In the current study the de novo and similarity-based methods allowed the identification for the first time of seven consensuses in M. destructor and two consensuses in M. hordei belonging to DD41D family whereas the in vitro method allowed the amplification of two and three elements in these two species respectively. Most of identified elements accumulated different mutations and long deletions spanning the N-terminal region of the transposase. Phylogenetic analyses showed that the DD41D elements were clustered in two groups belonging to rosa and Long-TIR subfamilies. The age estimation of the last transposition events of the identified Tc1/mariner elements in M. destructor showed different evolutionary histories. Indeed, irritans elements have oscillated between periods of silencing and reappearance while rosa and mauritiana elements have shown regular activity with large recent bursts. The study of insertion sites showed that they are mostly intronic and that some recently transposed elements occurred in genes linked to putative DNA-binding domains and enzymes involved in metabolic chains. Thus, this study gave evidence of the existence of DD41D family in two Mayetiola species and an insight on their evolutionary history.

Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.

CRISPR/dCas9-mediated transposition with specificity and efficiency of site-directed genomic insertions

The ability and efficiency of targeted nucleases to perform sequence replacements or insertions into the genome are limited. This limited efficiency for sequence replacements or insertions can be explained by the dependency on DNA repair pathways, the possibility of cellular toxicity, and unwanted activation of proto-oncogenes. The piggyBac (PB) transposase uses a very efficient enzymatic mechanism to integrate DNA fragments into the genome in a random manner. In this study, we fused an RNA-guided catalytically inactive Cas9 (dCas9) to the PB transposase and used dual sgRNAs to localize this molecule to specific genomic targets. We designed and used a promoter/reporter complementation assay to register and recover cells harboring-specific integrations, where only by complementation upon correct genomic integration, the reporter can be activated. Using an RNA-guided piggyBac transposase and dual sgRNAs, we were able to achieve site-directed integrations in the human ROSA26 safe harbor region in 0.32% of cells. These findings show that the methodology used in this study can be used for targeting genomic regions. An application for this finding could be in cancer cells to insert sequences into specific target regions that are intended to be destroyed, or to place promoter cargos behind the tumor suppressor genes to activate them.

Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements

Background

Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity.

Results

We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily.

Conclusions

Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.

Successful Invasions of Short Internally Deleted Elements (SIDEs) and Its Partner CR1 in Lepidoptera Insects

Although DNA transposons often generated internal deleted derivatives such as miniature inverted-repeat transposable elements, short internally deleted elements (SIDEs) derived from nonlong terminal-repeat retrotransposons are rare. Here, we found a novel SIDE, named Persaeus, that originated from the chicken repeat 1 (CR1) retrotransposon Zenon and it has been found widespread in Lepidoptera insects. Our findings suggested that Persaeus and the partner Zenon have experienced a transposition burst in their host genomes and the copy number of Persaeus and Zenon in assayed genomes are significantly correlated. Accordingly, the activity though age analysis indicated that the replication wave of Persaeus coincided with that of Zenon. Phylogenetic analyses suggested that Persaeus may have evolved at least four times independently, and that it has been vertically transferred into its host genomes. Together, our results provide new insights into the evolution dynamics of SIDEs and its partner non-LTRs.

Diversity and evolution of mariner-like elements in aphid genomes

Background

Although transposons have been identified in almost all organisms, genome-wide information on mariner elements in Aphididae remains unknown. Genomes of Acyrthosiphon pisum, Diuraphis noxia and Myzus persicae belonging to the Macrosiphini tribe, actually available in databases, have been investigated.

Results

A total of 22 lineages were identified. Classification and phylogenetic analysis indicated that they were subdivided into three monophyletic groups, each of them containing at least one putative complete sequence, and several non-autonomous sublineages corresponding to Miniature Inverted-Repeat Transposable Elements (MITE), probably generated by internal deletions. A high proportion of truncated and dead copies was also detected. The three clusters can be defined from their catalytic site: (i) mariner DD34D, including three subgroups of the irritans subfamily (Macrosiphinimar, Batmar-like elements and Dnomar-like elements); (ii) rosa DD41D, found in A. pisum and D. noxia; (iii) a new clade which differs from rosa through long TIRs and thus designated LTIR-like elements. Based on its catalytic domain, this new clade is subdivided into DD40D and DD41D subgroups. Compared to other Tc1/mariner superfamily sequences, rosa DD41D and LTIR DD40-41D seem more related to maT DD37D family.

Conclusion

Overall, our results reveal three clades belonging to the irritans subfamily, rosa and new LTIR-like elements. Data on structure and specific distribution of these transposable elements in the Macrosiphini tribe contribute to the understanding of their evolutionary history and to that of their hosts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3856-6) contains supplementary material, which is available to authorized users.

Characterization of mariner-like transposons of the mauritiana Subfamily in seven tree aphid species

Mariner-like elements (MLEs) are Class II transposons present in all eukaryotic genomes in which MLEs have been searched for. This article reports the detection of MLEs in seven of the main fruit tree aphid species out of eight species studied. Deleted MLE sequences of 916-919 bp were characterized, using the terminal-inverted repeats (TIRs) of mariner elements belonging to the mauritiana Subfamily as primers. All the sequences detected were deleted copies of full-length elements that included the 3'- and 5'-TIRs but displayed internal deletions affecting Mos1 activity. Networks based on the mtDNA cytochrome oxidase subunit-I (CO-I) and MLE sequences were incongruent, suggesting that mutations in transposon sequences had accumulated before speciation of tree aphid species occurred, and that they have been maintained in this species via vertical transmissions. This is the first evidence of the widespread occurrence of MLEs in aphids.

Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae

Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences.

Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA

The genome size in eukaryotes does not correlate well with the number of genes they contain. We can observe this so-called C-value paradox in amphibian species. By analyzing an amphibian genome we asked how repetitive DNA can impact genome size and architecture. We describe here our discovery of a Tc1/mariner miniature inverted-repeat transposon family present in Xenopus frogs. These transposons named miDNA4 are unique since they contain a satellite DNA motif. We found that miDNA4 measured 331 bp, contained 25 bp long inverted terminal repeat sequences and a sequence motif of 119 bp present as a unique copy or as an array of 2-47 copies. We characterized the structure, dynamics, impact and evolution of the miDNA4 family and its satellite DNA in Xenopus frog genomes. This led us to propose a model for the evolution of these two repeated sequences and how they can synergize to increase genome size.

Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins

The centromere is a chromatin region that is required for accurate inheritance of eukaryotic chromosomes during cell divisions. Among the different centromere-associated proteins (CENP) identified, CENP-B has been independently domesticated from a pogo-like transposase twice: Once in mammals and once in fission yeast. Recently, a third independent domestication restricted to holocentric lepidoptera has been described. In this work, we take advantage of the high-quality genome sequence and the wealth of functional information available for Drosophila melanogaster to further investigate the possibility of additional independent domestications of pogo-like transposases into host CENP-B related proteins. Our results showed that CENP-B related genes are not restricted to holocentric insects. Furthermore, we showed that at least three independent domestications of pogo-like transposases have occurred in metazoans. Our results highlight the importance of transposable elements as raw material for the recurrent evolution of important cellular functions.

Tc1-like transposable elements in plant genomes

BACKGROUND

The Tc1/mariner superfamily of transposable elements (TEs) is widespread in animal genomes. Mariner-like elements, which bear a DDD triad catalytic motif, have been identified in a wide range of flowering plant species. However, as the founding member of the superfamily, Tc1-like elements that bear a DD34E triad catalytic motif are only known to unikonts (animals, fungi, and Entamoeba).

RESULTS

Here we report the identification of Tc1-like elements (TLEs) in plant genomes. These elements bear the four terminal nucleotides and the characteristic DD34E triad motif of Tc1 element. The two TLE families (PpTc1, PpTc2) identified in the moss (Physcomitrella patens) genome contain highly similar copies. Multiple copies of PpTc1 are actively transcribed and the transcripts encode intact full length transposase coding sequences. TLEs are also found in angiosperm genome sequence databases of rice (Oryza sativa), dwarf birch (Betula nana), cabbage (Brassica rapa), hemp (Cannabis sativa), barley (Hordium valgare), lettuce (Lactuta sativa), poplar (Populus trichocarpa), pear (Pyrus x bretschneideri), and wheat (Triticum urartu).

CONCLUSIONS

This study extends the occurrence of TLEs to the plant phylum. The elements in the moss genome have amplified recently and may still be capable of transposition. The TLEs are also present in angiosperm genomes, but apparently much less abundant than in moss.