Penelope-like elements – a new class of retroelements: distribution, function and possible evolutionary significance

Genomic and Epidemiological Investigations Reveal Chromosomal Integration of the Acipenserid Herpesvirus 3 Genome in Lake Sturgeon Acipenser fulvescens

DNA sequence from a new alloherpesvirus named acipenserid herpesvirus 3 (AciHV-3) was found in sturgeon species that are vulnerable to decline globally. A study was undertaken to develop a better understanding of the virus genome and to develop diagnostic tools to support an epidemiological investigation. A 184,426 bp genome was assembled from PacBio HiFi sequences generated with DNA from a Lake Sturgeon Acipenser fulvescens gonad cell line. The AciHV-3 genome was contiguous with host chromosomal DNA and was structured with telomere-like terminal direct repeat regions, five internal direct repeat regions and a U region that included intact open reading frames encoding alloherpesvirus core proteins. Diagnostic testing conducted with a newly developed and analytically validated qPCR assay established the ubiquitous presence and high titer of AciHV-3 DNA in somatic and germline tissues from wild Lake Sturgeon in the Hudson Bay drainage basin. Phylogenetic reconstructions confirm that the monophyletic AciHV-3 lineage shares a common ancestor with AciHV-1 and that AciHV-3 taxa cluster according to their sturgeon host. The same genotype of AciHV-3 is found in disjunctive Lake Sturgeon populations within and among drainage basins. The results support the hypotheses that AciHV-3 has established latency through germline chromosomal integration, is vertically transmitted via a Mendelian pattern of inheritance, is evolving in a manner consistent with a replication competent virus and has co-evolved with its host reaching genetic fixation in Lake Sturgeon populations in central Canada.

Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae

The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies.

A beginner's guide to manual curation of transposable elements

BACKGROUND

In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill.

RESULTS

Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods.

CONCLUSIONS

The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs.

Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus

BACKGROUND

Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly (Danaus plexippus), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome.

RESULTS

We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes, Danaus chrysippus (33.97% TE) and Danaus melanippus (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and Penelope-like elements, and three newly identified families, r2-hero_dPle (LINE), penelope-1_dPle (Penelope-like), and hase2-1_dPle (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales (tc1-1_dPle, tc1-2_dPle). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes.

CONCLUSIONS

We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related Danaus species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

Diversity and Evolution of DNA Transposons Targeting Multicopy Small RNA Genes from Actinopterygian Fish

Simple Summary

DNA transposons are parasitic DNA segments that can move or duplicate themselves from one site to another in the genome. Dada is a unique group of DNA transposons, which specifically insert themselves into multicopy RNA genes such as transfer RNA (tRNA) genes or small nuclear RNA (snRNA) genes to avoid the disruption of single-copy functional genes. However, only a few Dada families have been characterized along with their target sequences. Here, vertebrate genomes were surveyed to characterize new Dada transposons, and over 120 Dada families were characterized from diverse fishes. They were classified into 12 groups with confirmed target specificities. Various tRNA genes, as well as 5S ribosomal RNA (rRNA) genes were inserted by Dada transposons. Phylogenetic analysis revealed that Dada transposons inserted in the same RNA genes are closely related. Phylogenetically related Dada transposons inserted in different RNA genes show the sequence similarity around their insertion sites, indicating Dada proteins recognize DNA nucleotide sequences to find their targets. Understanding how Dada discovers the targets would help develop target-specific insertions of foreign DNA segments.

Abstract

Dada is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of Dada transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. Dada-U6, which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize Dada families with new target specificities, and over 120 Dada families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized Dada families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian Dada families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related Dada families show sequence similarities, indicating that the target specificity of Dada is accomplished through the recognition of primary nucleotide sequences.

DARTS: An Algorithm for Domain-Associated Retrotransposon Search in Genome Assemblies

Retrotransposons comprise a substantial fraction of eukaryotic genomes, reaching the highest proportions in plants. Therefore, identification and annotation of retrotransposons is an important task in studying the regulation and evolution of plant genomes. The majority of computational tools for mining transposable elements (TEs) are designed for subsequent genome repeat masking, often leaving aside the element lineage classification and its protein domain composition. Additionally, studies focused on the diversity and evolution of a particular group of retrotransposons often require substantial customization efforts from researchers to adapt existing software to their needs. Here, we developed a computational pipeline to mine sequences of protein-coding retrotransposons based on the sequences of their conserved protein domains—DARTS (Domain-Associated Retrotransposon Search). Using the most abundant group of TEs in plants—long terminal repeat (LTR) retrotransposons (LTR-RTs)—we show that DARTS has radically higher sensitivity for LTR-RT identification compared to the widely accepted tool LTRharvest. DARTS can be easily customized for specific user needs. As a result, DARTS returns a set of structurally annotated nucleotide and amino acid sequences which can be readily used in subsequent comparative and phylogenetic analyses. DARTS may facilitate researchers interested in the discovery and detailed analysis of the diversity and evolution of retrotransposons, LTR-RTs, and other protein-coding TEs.

An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes

Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.

A Field Guide to Eukaryotic Transposable Elements

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.

Mobile Elements in Ray-Finned Fish Genomes

Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.

Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function

Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.

MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies

Background

Genomes of eukaryotes are inhabited by myriads of mobile genetic elements (MGEs) – transposons and retrotransposons - which play a great role in genome plasticity and evolution. A lot of computational tools were developed to annotate them either in genomic assemblies or raw reads using de novo or homology-based approaches. But there has been no pipeline enabling users to get coding and flanking sequences of MGEs suitable for a downstream analysis from genome assemblies.

Results

We developed a new pipeline, MGERT (Mobile Genetic Elements Retrieving Tool), that automates all the steps necessary to obtain protein-coding sequences of mobile genetic elements from genomic assemblies even if no previous knowledge on MGE content of a particular genome is available.

Conclusions

Using MGERT, researchers can easily find MGEs, their coding and flanking sequences in the genome of interest. Thus, this pipeline helps researchers to focus on the biological analysis of MGEs rather than excessive scripting and pipelining.

Electronic supplementary material

The online version of this article (10.1186/s13100-019-0163-6) contains supplementary material, which is available to authorized users.

Giant Transposons in Eukaryotes: Is Bigger Better?

Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics

Most genomes are populated by hundreds of thousands of sequences originated from mobile elements. On the one hand, these sequences present a real challenge in the process of genome analysis and annotation. On the other hand, they are very interesting biological subjects involved in many cellular processes. Here we present an overview of transposable elements biodiversity, and we discuss different approaches to transposable elements detection and analyses.

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes. A tripartite TE classification scheme is proposed to account for their replicative, integrative, and structural components, and the need to expand in vitro and in vivo studies of their structural and biological properties is emphasized. Bioinformatic studies have now become front and center of novel TE discovery, and experimental pursuits of these discoveries hold great promise for both basic and applied science.

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres

Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3′-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3′-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer.

Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers

Hammerhead ribozymes represent the most common of the 9 natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis. Herein, we report the discovery of ∼150,000 additional variant hammerhead representatives that exhibit diminished stem III substructures. These variants are frequently associated with Penelope-like retrotransposons, which are a type of mobile genetic element. Kinetic analyses indicate that these RNAs form dimers to cleave RNA.

Drosophila: Retrotransposons Making up Telomeres

Drosophila and extant species are the best-studied telomerase exception. In this organism, telomere elongation is coupled with targeted retrotransposition of Healing Transposon (HeT-A) and Telomere Associated Retrotransposon (TART) with sporadic additions of Telomere Associated and HeT-A Related (TAHRE), all three specialized non-Long Terminal Repeat (non-LTR) retrotransposons. These three very special retroelements transpose in head to tail arrays, always in the same orientation at the end of the chromosomes but never in interior locations. Apparently, retrotransposon and telomerase telomeres might seem very different, but a detailed view of their mechanisms reveals similarities explaining how the loss of telomerase in a Drosophila ancestor could successfully have been replaced by the telomere retrotransposons. In this review, we will discover that although HeT-A, TART, and TAHRE are still the only examples to date where their targeted transposition is perfectly tamed into the telomere biology of Drosophila, there are other examples of retrotransposons that manage to successfully integrate inside and at the end of telomeres. Because the aim of this special issue is viral integration at telomeres, understanding the base of the telomerase exceptions will help to obtain clues on similar strategies that mobile elements and viruses could have acquired in order to ensure their survival in the host genome.

LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types

Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3'-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.

An Unexplored Diversity of Reverse Transcriptases in Bacteria

Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations.

Transposable elements (TEs) are selfish elements that copy themselves. More than half of the human genome is comprised of such elements. Studies in the fruit flies Drosophila melanogaster and D. virilis have been important in demonstrating a role for RNA silencing by PIWI-interacting RNAs (piRNAs) in protecting the genome against these harmful elements. These small RNAs are capable of recognizing TE mRNAs and mediating their destruction. They are also transmitted by the female germline to offspring in order to maintain a stable genome across generations. When males carrying a particular TE family are crossed with females lacking the element, the mother is unable to provide genome defense via complementary piRNAs that target the element. This leads to excess TE activation in the germline and sterility, a phenomenon known as hybrid dysgenesis. In this article we characterize the genomic landscape of TE destabilization that occurs in dysgenic crosses of D. virilis. We demonstrate that this mobilization is associated with an increased level of germline TE expression that persists through adulthood. In addition, we find that TE activation is associated with diverse effects on normal gene expression that are also mediated by piRNAs.

Virus world as an evolutionary network of viruses and capsidless selfish elements

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

What happens when Penelope comes?: An unusual retroelement invades a host species genome exploring different strategies

Transposable elements (TEs) are ubiquitous residents in eukaryotic genomes. They can cause dramatic changes in gene expression and lead to gross rearrangements of chromosome structure, providing the basis for rapid evolution. The virilis species group of Drosophila contains certain species that can be crossed under experimental conditions and their phylogeny is thoroughly investigated. We have shown that Drosophila virilis, the most primitive karyotypically and probably the ancestral species of the group, is in the process of colonization by a very unusual retroelement Penelope which apparently repeatedly invaded the species of the group in the past. However, the molecular mechanisms and evolutionary consequences of such invasions are poorly understood. In this commentary, we discuss the implications of our recent investigation into the response of the RNA silencing system to Penelope invasion of a new host genome which can be achieved in different ways.

Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs

Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae

The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome

BACKGROUND

Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats.

RESULTS

Here we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed.

CONCLUSION

Using in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families

Background

Penelope-like elements (PLEs) are an enigmatic group of retroelements sharing a common ancestor with telomerase reverse transcriptases. In our previous studies, we identified endonuclease-deficient PLEs that are associated with telomeres in bdelloid rotifers, small freshwater invertebrates best known for their long-term asexuality and high foreign DNA content. Completion of the high-quality draft genome sequence of the bdelloid rotifer Adineta vaga provides us with the opportunity to examine its genomic transposable element (TE) content, as well as TE impact on genome function and evolution.

Results

We performed an exhaustive search of the A. vaga genome assembly, aimed at identification of canonical PLEs combining both the reverse transcriptase (RT) and the GIY-YIG endonuclease (EN) domains. We find that the RT/EN-containing Penelope families co-exist in the A. vaga genome with the EN-deficient RT-containing Athena retroelements. Canonical PLEs are present at very low copy numbers, often as a single-copy, and there is no evidence that they might preferentially co-mobilize EN-deficient PLEs. We also find that Penelope elements can participate in expansion of A. vaga multigene families via trans-action of their enzymatic machinery, as evidenced by identification of intron-containing host genes framed by the Penelope terminal repeats and characteristic target-site duplications generated upon insertion. In addition, we find that Penelope open reading frames (ORFs) in several families have incorporated long stretches of coding sequence several hundred amino acids (aa) in length that are highly enriched in asparagine residues, a phenomenon not observed in other retrotransposons.

Conclusions

Our results show that, despite their low abundance and low transcriptional activity in the A. vaga genome, endonuclease-containing Penelope elements can participate in expansion of host multigene families. We conclude that the terminal repeats represent the cis-acting sequences required for mobilization of the intervening region in trans by the Penelope-encoded enzymatic activities. We also hypothesize that the unusual capture of long N-rich segments by the Penelope ORF occurs as a consequence of peculiarities of its replication mechanism. These findings emphasize the unconventional nature of Penelope retrotransposons, which, in contrast to all other retrotransposon types, are capable of dispersing intron-containing genes, thereby questioning the validity of traditional estimates of gene retrocopies in PLE-containing eukaryotic genomes.

Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids

Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.

Endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon and related retroelements: a new model for transposition

The molecular mechanisms of the transposition of non-long terminal repeat (non-LTR) retrotransposons are not well understood; the key questions of how the 3′-ends of cDNA copies integrate and how site-specific integration occurs remain unresolved. Integration depends on properties of the endonuclease (EN) domain of retrotransposons. Using the EN domain of the Drosophila R2 retrotransposon as a model for other, closely related non-LTR retrotransposons, we investigated the EN domain and found that it resembles archaeal Holliday-junction resolvases. We suggest that these non-LTR retrotransposons are co-transcribed with the host transcript. Combined with the proposed resolvase activity of the EN domain, this model yields a novel mechanism for site-specific retrotransposition within this class of retrotransposons, with resolution proceeding via a Holliday junction intermediate.

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Background

Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability.

The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible.

Results

Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups.

Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region.

The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening.

The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny.

Conclusion

The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.

Identification of two Penelope-like elements with different structures and chromosome localization in kuruma shrimp genome

Penelope, originally found as a key element responsible for the hybrid dysgenesis in Drosophila virilis, has been widely conserved throughout eukaryotic genomes. In other organisms, they are often referred to as Penelope-like elements or PLEs. In this study, we found two types of PLEs, designated MjPLE01 and MjPLE02, from kuruma shrimp, Marsupenaeus japonicus. There was no observed nucleotide similarity between MjPLE01 and 02, and both elements differed from each other in terms of their structure; MjPLE02 has a distinctive endonuclease (EN) domain at the C-terminus while MjPLE01 do not. A phylogenetic tree that includes publicly available PLEs and TERTs showed that MjPLE01 and 02 were closely related to Coprina elements, which have been reported as an EN-deficient PLE, and to Penelope-Poseidon group, which possess an EN domain, respectively. Genomic Southern blot analysis using MjPLE01 as a probe showed several multiple bands that differ among individual shrimps. On the other hand, two major identical bands were observed when MjPLE02 was used. Colony hybridization showed co-localization of MjPLE01 and GGTTA repeats, suggesting that MjPLE01 might be prevalent in subtelomeric regions of kuruma shrimp genome. These results suggest that the kuruma shrimp genome has at least two types of PLEs with different domain compositions, phylogenetic positions, and probably chromosomeal localization. Such distinctive types of PLEs in an organism have never been described and hence could be a potential source to understand how multiple PLE types evolved.

Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila

Although small RNAs efficiently control transposition activity of most transposons in the host genome, such an immune system is not always applicable against a new transposon's invasions. Here, we explored a possibility to introduce potentially mobile copy of the Penelope retroelement previously implicated in hybrid dysgenesis syndrome in Drosophila virilis into the genomes of two distant Drosophila species. The consequences of such introduction were monitored at different phases after experimental colonization as well as in D. virilis species, which is apparently in the process of ongoing Penelope invasion. We investigated the expression of Penelope and biogenesis of Penelope-derived small RNAs in D. virilis and D. melanogaster strains originally lacking active copies of this element after experimental Penelope invasion. These strains were transformed by constructs containing intact Penelope copies. We show that immediately after transformation, which imitates the first stage of retroelement invasion, Penelope undergoes transposition predominantly in somatic tissues, and may produce siRNAs that are apparently unable to completely silence its activity. However, at the later stages of colonization Penelope copies may jump into one of the piRNA-clusters, which results in production of homologous piRNAs that are maternally deposited and can silence euchromatic transcriptionally active copies of Penelope in trans and, hence, prevent further amplification of the invader in the host genome. Intact Penelope copies and different classes of Penelope-derived small RNAs were found in most geographical strains of D. virilis collected throughout the world. Importantly, all strains of this species containing full-length Penelope tested do not produce gonadal sterility in dysgenic crosses and, hence, exhibit neutral cytotype. To understand whether RNA interference mechanism able to target Penelope operates in related species of the virilis group, we correlated the presence of full-length and potentially active Penelope with the occurrence of piRNAs homologous to this transposable element in the ovaries of species comprising the group. It was demonstrated that Penelope-derived piRNAs are present in all virilis group species containing full-length but transcriptionally silent copies of this element that probably represent the remnants of its previous invasions taking place in the course of the virilis species divergent evolution.

Transposable elements: from DNA parasites to architects of metazoan evolution

One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.

The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo

The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) defines a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF). Here, we describe a LEM protein annotated in databases as 'Ankyrin repeat and LEM domain-containing protein 1' (Ankle1). We show that Ankle1 is conserved in metazoans and contains a unique C-terminal GIY-YIG motif that confers endonuclease activity in vitro and in vivo. In mammals, Ankle1 is predominantly expressed in hematopoietic tissues. Although most characterized LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. Ankle1 enriched in the nucleoplasm induces DNA cleavage and DNA damage response. This activity requires both the catalytic C-terminal GIY-YIG domain and the LEM motif, which binds chromatin via BAF. Hence, Ankle1 is an unusual LEM protein with a GIY-YIG-type endonuclease activity in higher eukaryotes.

Transposable elements and their identification

Most genomes are populated by thousands of sequences that originated from mobile elements. On the one hand, these sequences present a real challenge in the process of genome analysis and annotation. On the other hand, there are very interesting biological subjects involved in many cellular processes. Here, we present an overview of transposable elements (TEs) biodiversity and their impact on genomic evolution. Finally, we discuss different approaches to the TEs detection and analyses.

Single-stranded DNA repeat synthesis by telomerase

The eukaryotic ribonucleoprotein reverse transcriptase (RT) telomerase uses a template within its integral RNA subunit to extend chromosome ends by synthesis of single-stranded telomeric repeats. Telomerase is adapted to its unique cellular role by an ability to release product DNA in single-stranded form, regenerating free template from the product-template hybrid. Furthermore, by retaining a template-independent grip on the single-stranded product, telomerase can catalyze processive repeat synthesis. These specialized nucleic acid handling properties are dependent on the protein and RNA domain network within an active RNP. RNP domain architecture and mechanisms for single-stranded DNA handling have been a focus of recent studies highlighted here.

Expression of Drosophila virilis retroelements and role of small RNAs in their intrastrain transposition

Transposition of two retroelements (Ulysses and Penelope) mobilized in the course of hybrid dysgenesis in Drosophila virilis has been investigated by in situ hybridization on polytene chromosomes in two D. virilis strains of different cytotypes routinely used to get dysgenic progeny. The analysis has been repeatedly performed over the last two decades, and has revealed transpositions of Penelope in one of the strains, while, in the other strain, the LTR-containing element Ulysses was found to be transpositionally active. The gypsy retroelement, which has been previously shown to be transpositionally inactive in D. virilis strains, was also included in the analysis. Whole mount is situ hybridization with the ovaries revealed different subcellular distribution of the transposable elements transcripts in the strains studied. Ulysses transpositions occur only in the strain where antisense piRNAs homologous to this TE are virtually absent and the ping-pong amplification loop apparently does not take place. On the other hand small RNAs homologous to Penelope found in the other strain, belong predominantly to the siRNA category (21nt), and consist of sense and antisense species observed in approximately equal proportion. The number of Penelope copies in the latter strain has significantly increased during the last decades, probably because Penelope-derived siRNAs are not maternally inherited, while the low level of Penelope-piRNAs, which are faithfully transmitted from mother to the embryo, is not sufficient to silence this element completely. Therefore, we speculate that intrastrain transposition of the three retroelements studied is controlled predominantly at the post-transcriptional level.

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

Background

The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses.

Results

We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome.

Conclusions

The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.

How many antiviral small interfering RNAs may be encoded by the mammalian genomes?

Background

The discovery of RNA interference phenomenon (RNAi) and understanding of its mechanisms has revolutionized our views on many molecular processes in the living cell. Among the other, RNAi is involved in silencing of transposable elements and in inhibition of virus infection in various eukaryotic organisms. Recent experimental studies demonstrate few cases of viral replication suppression via complementary interactions between the mammalian small RNAs and viral transcripts.

Presentation of the hypothesis

It was found that >50% of the human genome is transcribed in different cell types and that these transcripts are mainly not associated with known protein coding genes, but represent non-coding RNAs of unknown functions. We propose a hypothesis that mammalian DNAs encode thousands RNA motifs that may serve for antiviral protection. We also presume that the evolutional success of some groups of genomic repeats and, in particular, of transposable elements (TEs) may be due to their ability to provide antiviral RNA motifs to the host organism. Intense genomic repeat propagation into the genome would inevitably cause bidirectional transcription of these sequences, and the resulting double-stranded RNAs may be recognized and processed by the RNA interference enzymatic machinery. Provided that these processed target motifs may be complementary to viral transcripts, fixation of the repeats into the host genome may be of a considerable benefit to the host. It fits with our bioinformatical data revealing thousands of 21-28 bp long motifs identical between human DNA and human-pathogenic adenoviral and herpesviral genomes. Many of these motifs are transcribed in human cells, and the transcribed part grows proportionally to their lengths. Many such motifs are included in human TEs. For example, one 23 nt-long motif that is a part of human abundant Alu retrotransposon, shares sequence identity with eight human adenoviral genomes.

Testing the hypothesis

This hypothesis could be tested on various mammalian species and viruses infecting mammalian cells.

Implications of the hypothesis

This hypothesis proposes that mammalian organisms may use their own genomes as sources of thousands of putative interfering RNA motifs that can be recruited to repress intracellular pathogens like proliferating viruses.

Reviewers

This article was reviewed by Eugene V. Koonin, Valerian V. Dolja and Yuri V. Shpakovski.

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

Colonization of a host by an active transposon can increase mutation rates or cause sterility, a phenotype termed hybrid dysgenesis. As an example, intercrosses of certain Drosophila virilis strains can produce dysgenic progeny. The Penelope element is present only in a subset of laboratory strains and has been implicated as a causative agent of the dysgenic phenotype. We have also introduced Penelope into Drosophila melanogaster, which are otherwise naive to the element. We have taken advantage of these natural and experimentally induced colonization processes to probe the evolution of small RNA pathways in response to transposon challenge. In both species, Penelope was predominantly targeted by endo-small-interfering RNAs (siRNAs) rather than by piwi-interacting RNAs (piRNAs). Although we do observe correlations between Penelope transcription and dysgenesis, we could not correlate differences in maternally deposited Penelope piRNAs with the sterility of progeny. Instead, we found that strains that produced dysgenic progeny differed in their production of piRNAs from clusters in subtelomeric regions, possibly indicating that changes in the overall piRNA repertoire underlie dysgenesis. Considered together, our data reveal unexpected plasticity in small RNA pathways in germ cells, both in the character of their responses to invading transposons and in the piRNA clusters that define their ability to respond to mobile elements.

The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

Background

Sadhu elements are non-autonomous retroposons first recognized in Arabidopsis thaliana. There is a wide degree of divergence among different elements, suggesting that these sequences are ancient in origin. Here we report the results of several lines of investigation into the genomic organization and evolutionary history of this element family.

Results

We present a classification scheme for Sadhu elements in A. thaliana, describing derivative elements related to the full-length elements we reported previously. We characterized Sadhu5 elements in a set of A. thaliana strains in order to trace the history of radiation in this subfamily. Sequences surrounding the target sites of different Sadhu insertions are consistent with mobilization by LINE retroelements. Finally, we identified Sadhu elements grouping into distinct subfamilies in two related species, Arabidopsis arenosa and Arabidopsis lyrata.

Conclusions

Our analyses suggest that the Sadhu retroelement family has undergone target primed reverse transcription-driven retrotransposition during the divergence of different A. thaliana strains. In addition, Sadhu elements can be found at moderate copy number in three distinct Arabidopsis species, indicating that the evolutionary history of these sequences can be traced back at least several millions of years.

Unique functions of repetitive transcriptomes

Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.

Retroelements and their impact on genome evolution and functioning

Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.

Transposable elements and factors influencing their success in eukaryotes

Recent advances in genome sequencing have led to a vast accumulation of transposable element data. Consideration of the genome sequencing projects in a phylogenetic context reveals that despite the hundreds of eukaryotic genomes that have been sequenced, a strong bias in sampling exists. There is a general under-representation of unicellular eukaryotes and a dearth of genome projects in many branches of the eukaryotic phylogeny. Among sequenced genomes, great variation in genome size exists, however, little difference in the total number of cellular genes is observed. For many eukaryotes, the remaining genomic space is extremely dynamic and predominantly composed of a menagerie of populations of transposable elements. Given the dynamic nature of the genomic niche filled by transposable elements, it is evident that these elements have played an important role in genome evolution. The contribution of transposable elements to genome architecture and to the advent of genetic novelty is likely to be dependent, at least in part, on the transposition mechanism, diversity, number, and rate of turnover of transposable elements in the genome at any given time. The focus of this review is the discussion of some of the forces that act to shape transposable element diversity within and between genomes.

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on a rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 min on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1).

Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard

Hox genes control many aspects of embryonic development in metazoans. Previous analyses of this gene family revealed a surprising diversity in terms of gene number and organization between various animal species. In vertebrates, Hox genes are grouped into tightly organized clusters, claimed to be devoid of repetitive sequences. Here, we report the genomic organization of the four Hox loci present in the green anole lizard and show that they have massively accumulated retrotransposons, leading to gene clusters larger in size when compared to other vertebrates. In addition, similar repeats are present in many other development-related gene-containing regions, also thought to be refractory to such repetitive elements. Transposable elements are major sources of genetic variations, including alterations of gene expression, and hence this situation, so far unique among vertebrates, may have been associated with the evolution of the spectacular realm of morphological variations in the body plans of Squamata. Finally, sequence alignments highlight some divergent evolution in highly conserved DNA regions between vertebrate Hox clusters, which may coincide with the emergence of mammalian-specific features.

Evidence of multiple retrotransposons in two litopenaeid species

Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon.