scholarly journals Transposable Elements and the Evolution of Insects

2021 ◽  
Vol 66 (1) ◽  
pp. 355-372
Author(s):  
Clément Gilbert ◽  
Jean Peccoud ◽  
Richard Cordaux

Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.

2020 ◽  
Author(s):  
Kakeru Yokoi ◽  
Kiyoshi Kimura ◽  
Hidemasa Bono

AbstractBackgroundMariner and mariner-like elements (MLEs) are distributed in various species and their sequences are highly diverse. In previous reports, a few transposable element in the genomes of Apis species mainly consist of mariner and MLE. For further insight of Apis MLEs, detailed classifications of Apis MLE and sequences analysis of long MLEs, which may potentially encode the transposase, are needed.ResultsMuch more MLEs were detected in A. mellifera genome compared to other Apis species genomes. They were classified into 31 Drosophila MLE classes. In this classification, almost all of MLEs were classified into the three classes belonging to mellifera subfamilies, suggesting that Apis MLEs which exist thorough Apis species derived from single MLE belonging to mellifera subfamily. Phylogenetic analysis using MLEs in the three classes showed that there two types of clusters, of which one consist of multiple Apis species MLEs, and others of only A. mellifera MLEs. Long MLEs analysis showed that only one long MLE encoding complete transposase was found in all Apis genome except for A. mellifera genome, and the MLE and multiple MLEs similar to it were found in A. mellifera genome. The analysis also showed that other several long MLEs encoding complete transposase were found only in A. mellifera genome.ConclusionsAlmost all of Apis MLEs are mellifera subfamilies. Of these MLEs, one types of them settled in Apis species and burst in A. mellifera genome. The other one of MLEs invaded into A. mellifera genome by horizontal transfer and exploded in A. mellifera genome. This is the first example of the finer aspects of MLE evolution among closely related species.


2000 ◽  
Vol 68 (12) ◽  
pp. 7180-7185 ◽  
Author(s):  
O. Colin Stine ◽  
Shanmuga Sozhamannan ◽  
Qing Gou ◽  
Siqen Zheng ◽  
J. Glenn Morris ◽  
...  

ABSTRACT We sequenced a 705-bp fragment of the recA gene from 113 Vibrio cholerae strains and closely related species. One hundred eighty-seven nucleotides were phylogenetically informative, 55 were phylogenetically uninformative, and 463 were invariant. Not unexpectedly, Vibrio parahaemolyticus and Vibrio vulnificus strains formed out-groups; we also identified isolates which resembled V. cholerae biochemically but which did not cluster with V. cholerae. In many instances, V. cholerae serogroup designations did not correlate with phylogeny, as reflected by recA sequence divergence. This observation is consistent with the idea that there is horizontal transfer of O-antigen biosynthesis genes among V. cholerae strains.


2017 ◽  
Vol 25 (01) ◽  
pp. 71-81
Author(s):  
YOUHUA CHEN

In theoretical ecology and community ecology, it is still unclear how phylogenetic community structure and species distributions are linked together. In this paper, a neutral model for evaluating phylogenetic constraints on species diversity and distribution patterns is developed to address these issues. To accomplish this, temporal species distribution and diversity patterns are evaluated and simulated by considering the impact of phylogenetic relatedness of species in a lattice landscape with square grids. A continuous patch for the resultant distributional range map of a species is defined as a group of grids in which the interior grids are adjacent to each other while the edge grids of the patch are isolated from other remaining grids in the range map. The adjacency or isolation of a grid with respect to another grid follows the von Neumann neighborhood criterion. The hypothesis tested is: phylogenetically closely related species tend to avoid each other (phylogenetic dilution), which produces a phylogenetic overdispersion pattern. In this case, all species have similar species abundances and distribution-patch size patterns. In contrast, if closely related species tend to associate together (phylogenetic concentration), a phylogenetic clustering pattern emerges: phylogenetically distinct species tend to have higher abundances and more large distribution patches. Using simulations, this paper presents results which demonstrate the reverse phenomenon: if it is assumed that phylogenetic relatedness of species is modeled as a dilution effect, the resultant distributional maps for evolutionarily distinct species present significantly increased numbers of continuous large patches. An evolutionarily distinct clade tends to have significantly higher relative abundance than other clades in all simulations. It was also found that if phylogenetic relatedness of species is modeled as a concentration effect, the simulated distributional map of each species would present a similar percentage of large patches for both evolutionarily unique and common clades for many cases when the community size is large enough. However, being similar to dilution effect, the resultant species relative abundance for evolutionarily unique clade is significantly higher than that for evolutionarily common clade. In conclusion, evolutionary distinct species will have more chances to survive with high populations and less fragmented distributional range in environments where the phylogenetic dilution effect is functioning. It is hoped that these results contributed to clarifying the complex associations generated by phylogenetic community structure in future ecological and evolutionary studies.


2017 ◽  
Vol 114 (18) ◽  
pp. 4721-4726 ◽  
Author(s):  
Jean Peccoud ◽  
Vincent Loiseau ◽  
Richard Cordaux ◽  
Clément Gilbert

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.


PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000689
Author(s):  
Christopher E. Ellison ◽  
Meenakshi S. Kagda ◽  
Weihuan Cao

Coevolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by reestablishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. The TART-A TE functions as an important component of Drosophila telomeres but has also reportedly inserted into the Drosophila melanogaster nuclear export factor gene nxf2. We find that, rather than inserting into nxf2, TART-A has actually captured a portion of nxf2 sequence. We show that TART-A produces abundant Piwi-interacting small RNAs (piRNAs), some of which are antisense to the nxf2 transcript, and that the TART-like region of nxf2 is evolving rapidly. Furthermore, in D. melanogaster, TART-A is present at higher copy numbers, and nxf2 shows reduced expression, compared to the closely related species Drosophila simulans. We propose that capturing nxf2 sequence allowed TART-A to target the nxf2 gene for piRNA-mediated repression and that these 2 elements are engaged in antagonistic coevolution despite the fact that TART-A is serving a critical role for its host genome.


2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock

Abstract Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.


Author(s):  
Cécile Lorrain ◽  
Alice Feurtey ◽  
Mareike Möller ◽  
Janine Haueisen ◽  
Eva Stukenbrock

AbstractTransposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires, suggesting variation in the efficacy of genome defences. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in thirteen genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The thirteen genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with distinct genome compartments in all Zymoseptoria species, including chromosomal rearrangements, genes showing presence/absence variation and effectors. European Z. tritici isolates have reduced signatures of Repeat-Induced Point mutations compared to Iranian isolates and closely related species. Our study supports the hypothesis that ongoing but moderate TE mobility in Zymoseptoria species shapes pathogen genome evolution.


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