scholarly journals Vertical Evolution and Horizontal Transfer of CR1 Non-LTR Retrotransposons and Tc1/mariner DNA Transposons in Lepidoptera Species

2012 ◽  
Vol 29 (12) ◽  
pp. 3685-3702 ◽  
Author(s):  
Irina Sormacheva ◽  
Georgiy Smyshlyaev ◽  
Vladimir Mayorov ◽  
Alexander Blinov ◽  
Anton Novikov ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Ltr Retrotransposons ◽  
Dna Transposons ◽  
Vertical Evolution

scholarly journals Incomer, a DD36E family of Tc1/mariner transposons newly discovered in animals

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yatong Sang ◽  
Bo Gao ◽  
Mohamed Diaby ◽  
Wencheng Zong ◽  
Cai Chen ◽  
...  
Keyword(s):  
Horizontal Transfer ◽  
Myotis Lucifugus ◽  
Pairwise Distance ◽  
Base Pairs ◽  
Dna Transposons ◽  
Reading Frame ◽  
Consensus Sequences ◽  
New Family ◽  
Copy Numbers ◽  
Close Relationship

Abstract Background The Tc1/mariner superfamily might represent the most diverse and widely distributed group of DNA transposons. Several families have been identified; however, exploring the diversity of this superfamily and updating its classification is still ongoing in the life sciences. Results Here we identified a new family of Tc1/mariner transposons, named Incomer (IC), which is close to, but distinct from the known family DD34E/Tc1. ICs have a total length of about 1.2 kb, and harbor a single open reading frame encoding a ~ 346 amino acid transposase with a DD36E motif and flanked by short terminal inverted repeats (TIRs) (22–32 base pairs, bp). This family is absent from prokaryotes, and is mainly distributed among vertebrates (141 species of four classes), including Agnatha (one species of jawless fish), Actinopterygii (132 species of ray-finned fish), Amphibia (four species of frogs), and Mammalia (four species of bats), but have a restricted distribution in invertebrates (four species in Insecta and nine in Arachnida). All ICs in bats (Myotis lucifugus, Eptesicus fuscus, Myotis davidii, and Myotis brandtii) are present as truncated copies in these genomes, and most of them are flanked by relatively long TIRs (51–126 bp). High copy numbers of miniature inverted-repeat transposable elements (MITEs) derived from ICs were also identified in bat genomes. Phylogenetic analysis revealed that ICs are more closely related to DD34E/Tc1 than to other families of Tc1/mariner (e.g., DD34D/mariner and DD × D/pogo), and can be classified into four distinct clusters. The host and IC phylogenies and pairwise distance comparisons between RAG1 genes and all consensus sequences of ICs support the idea that multiple episodes of horizontal transfer (HT) of ICs have occurred in vertebrates. In addition, the discovery of intact transposases, perfect TIRs and target site duplications of ICs suggests that this family may still be active in Insecta, Arachnida, frogs, and fish. Conclusions Exploring the diversity of Tc1/mariner transposons and revealing their evolutionary profiles will help provide a better understanding of the evolution of DNA transposons and their impact on genomic evolution. Here, a newly discovered family (DD36E/Incomer) of Tc1/mariner transposons is described in animals. It displays a similar structural organization and close relationship with the known DD34E/Tc1 elements, but has a relatively narrow distribution, indicating that DD36E/IC might have originated from the DD34E/Tc1 family. Our data also support the hypothesis of horizontal transfer of IC in vertebrates, even invading one lineage of mammals (bats). This study expands our understanding of the diversity of Tc1/mariner transposons and updates the classification of this superfamily.

scholarly journals A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jade Southworth ◽  
C. Alastair Grace ◽  
Alan O. Marron ◽  
Nazeefa Fatima ◽  
Martin Carr
Keyword(s):  
Transposable Elements ◽  
Codon Usage ◽  
Population Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Translational Efficiency ◽  
Ltr Retrotransposons ◽  
Dna Transposons ◽  
Show Evidence ◽  
Salpingoeca Rosetta

Abstract Background Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Results Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. Conclusions S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.

scholarly journals Evolution of multiple families of non-LTR retrotransposons in phlebotomine sandflies

1996 ◽  
Vol 67 (3) ◽  
pp. 227-237 ◽  
Author(s):  
David R. Booth ◽  
Paul D. Ready ◽  
Deborah F. Smith
Keyword(s):  
Intraspecific Variation ◽  
Copy Number ◽  
Sequence Divergence ◽  
Ltr Retrotransposons ◽  
Generic Level ◽  
Closely Related Species ◽  
Hybridization Pattern ◽  
Phlebotomine Sandflies ◽  
Vertical Evolution ◽  
Different Populations

SummaryIn this paper we report on the diversity and distribution of a set of non-LTR retrotransposon (RTP) reverse transcriptase (RT) sequences isolated from phlebotomine sandflies, and their potential for investigating the evolutionary histories of members of this subfamily of flies (Diptera: Psychodidae, Phlebotominae). The phlebotomine RT sequence families derived from one species were as different from each other as they were from RT sequences derived from other species. When each was used to probe Southern blots of sandfly genomic DNA they hybridized only to the species of source and, usually, to others of the same subgenus, but not to DNA from other subgenera — a hybridization pattern consistent with vertical evolution. There was considerable intraspecific variation in hybridization pattern, suggesting the RTs were part of non-LTR RTPs that are (or were recently) subject to flux in genomic position and copy number. Most of the RT families detected in phlebotomines are monophyletic with respect to previously described RTs, and all are monophyletic with RTs of the F/Jockey (Drosophila melanogaster) type of RTP. Orthologous sequences were isolated from the closely related species Phlebotomus perniciosus and P. tobbi (subgenus Larroussius), and different populations of P. perniciosus. The level of sequence divergence among these orthologous RTs, the subgeneric distribution of each RT family, and the intraspecific variation in hybridization pattern of many of them, indicate this class of sequence will provide genetic markers at the sub-generic level.

scholarly journals Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

2020 ◽  
Author(s):  
Yann Bourgeois ◽  
Robert Ruggiero ◽  
Imtiyaz Hariyani ◽  
Stéphane Boissinot
Keyword(s):  
Transposable Elements ◽  
Demographic History ◽  
Ltr Retrotransposons ◽  
Frequency Spectra ◽  
Dna Transposons ◽  
Genomic Landscape ◽  
Demographic Processes ◽  
History Of ◽  
Recent Phase ◽  
Positive Correlations

AbstractBackgroundThe interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons).ResultsWe observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation..ConclusionsWe demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

scholarly journals Multiple Non-LTR Retrotransposons in the Genome of Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 569-578 ◽  
Author(s):  
David A Wright ◽  
Ning Ke ◽  
Jan Smalle ◽  
Brian M Hauge ◽  
Howard M Goodman ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Reverse Transcriptase ◽  
Phylogenetic Analyses ◽  
Repetitive Sequences ◽  
Amino Acid Sequences ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Reverse Transcriptases ◽  
Highly Active ◽  
Vertical Evolution

Abstract DNA sequence analysis near the Arabidopsis thaliana AB13 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. This insertion is 6.2 kb in length and encodes two overlapping reading frames with similarity to non-LTR retrotransposon proteins, including reverse transcriptase. A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. Seventeen additional A. thaliana reverse transcriptases were identified that range in nucleotide similarity from 48–88% (Ta12-Ta28). Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The remaining are nuclear and of low copy number among 17 diverse A. thaliana ecotypes tested, suggesting that they are not highly active in transposition. The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families.

scholarly journals Identification and characterization of retro-DNAs, a new type of retrotransposons originated from DNA transposons, in primate genomes

2020 ◽  
Author(s):  
Wanxiangfu Tang ◽  
Ping Liang
Keyword(s):  
Dna Sequences ◽  
Insertion Site ◽  
Long Terminal Repeat Retrotransposons ◽  
Ltr Retrotransposons ◽  
Polya Tail ◽  
Dna Transposons ◽  
Dna Transposon ◽  
Processed Pseudogenes ◽  
New Type ◽  
Transposon Activity

AbstractMobile elements (MEs) can be divided into two major classes based on their transposition mechanisms as retrotransposons and DNA transposons. DNA transposons move in the genomes directly in the form of DNA in a cut-and-paste style, while retrotransposons utilize an RNA-intermediate to transpose in a “copy-and-paste” fashion. In addition to the target site duplications (TSDs), a hallmark of transposition shared by both classes, the DNA transposons also carry terminal inverted repeats (TIRs). DNA transposons constitute ~3% of primate genomes and they are thought to be inactive in the recent primate genomes since ~37My ago despite their success during early primate evolution. Retrotransposons can be further divided into Long Terminal Repeat retrotransposons (LTRs), which are characterized by the presence of LTRs at the two ends, and non-LTRs, which lack LTRs. In the primate genomes, LTRs constitute ~9% of genomes and have a low level of ongoing activity, while non-LTR retrotransposons represent the major types of MEs, contributing to ~37% of the genomes with some members being very young and currently active in retrotransposition. The four known types of non-LTR retrotransposons include LINEs, SINEs, SVAs, and processed pseudogenes, all characterized by the presence of a polyA tail and TSDs, which mostly range from 8 to 15 bp in length. All non-LTR retrotransposons are known to utilize the L1-based target-primed reverse transcription (TPRT) machineries for retrotransposition. In this study, we report a new type of non-LTR retrotransposon, which we named as retro-DNAs, to represent DNA transposons by sequence but non-LTR retrotransposons by the transposition mechanism in the recent primate genomes. By using a bioinformatics comparative genomics approach, we identified a total of 1,750 retro-DNAs, which represent 748 unique insertion events in the human genome and nine non-human primate genomes from the ape and monkey groups. These retro-DNAs, mostly as fragments of full-length DNA transposons, carry no TIRs but longer TSDs with ~23.5% also carrying a polyA tail and with their insertion site motifs and TSD length pattern characteristic of non-LTR retrotransposons. These features suggest that these retro-DNAs are DNA transposon sequences likely mobilized by the TPRT mechanism. Further, at least 40% of these retro-DNAs locate to genic regions, presenting significant potentials for impacting gene function. More interestingly, some retro-DNAs, as well as their parent sites, show certain levels of current transcriptional expression, suggesting that they have the potential to create more retro-DNAs in the current primate genomes. The identification of retro-DNAs, despite small in number, reveals a new mechanism in propagating the DNA transposons sequences in the primate genomes with the absence of canonical DNA transposon activity. It also suggests that the L1 TPRT machinery may have the ability to retrotranspose a wider variety of DNA sequences than what we currently know.

scholarly journals Prokaryotic and Eukaryotic Horizontal Transfer of Sailor (DD82E), a New Superfamily of IS630-Tc1-Mariner DNA Transposons

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1005
Author(s):  
Shasha Shi ◽  
Mikhail Puzakov ◽  
Zhongxia Guan ◽  
Kuilin Xiang ◽  
Mohamed Diaby ◽  
...  
Keyword(s):  
Strong Evidence ◽  
Horizontal Transfer ◽  
Catalytic Domain ◽  
Phylogenetic Analyses ◽  
Target Site ◽  
Monophyletic Clade ◽  
Dna Transposons ◽  
Intimate Link ◽  
Data Update

Here, a new superfamily of IS630-Tc1-mariner (ITm) DNA transposons, termed Sailor, is identified, that is characterized by a DD82E catalytic domain and is distinct from all previously known superfamilies of the ITm group. Phylogenetic analyses revealed that Sailor forms a monophyletic clade with a more intimate link to the clades of Tc1/mariner and DD34E/Gambol. Sailor was detected in both prokaryotes and eukaryotes and invaded a total of 256 species across six kingdoms. Sailor is present in nine species of bacteria, two species of plantae, four species of protozoa, 23 species of Chromista, 12 species of Fungi and 206 species of animals. Moreover, Sailor is extensively distributed in invertebrates (a total of 206 species from six phyla) but is absent in vertebrates. Sailor transposons are 1.38–6.98 kb in total length and encoded transposases of ~676 aa flanked by TIRs with lengths between 18, 1362 and 4 bp (TATA) target-site duplications. Furthermore, our analysis provided strong evidence of Sailor transmissions from prokaryotes to eukaryotes and internal transmissions in both. These data update the classification of the ITm group and will contribute to the understanding of the evolution of ITm transposons and that of their hosts.

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