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

Irina R Arkhipova*, Irina A Yushenova and Fernando Rodriguez

Author Affiliations

Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA

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Mobile DNA 2013, 4:19  doi:10.1186/1759-8753-4-19

The electronic version of this article is the complete one and can be found online at: http://www.mobilednajournal.com/content/4/1/19


Received:3 December 2012
Accepted:16 August 2013
Published:27 August 2013

© 2013 Arkhipova et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.

Keywords:
Retrotransposon; Reverse transcriptase; GIY-YIG endonuclease

Background

Penelope-like elements (PLEs) represent an ancient class of eukaryotic retroelements that shares a common ancestor with telomerase reverse transcriptases [1,2]. They can be found in protists, fungi, animals and plants, although their representation in these taxa can be very sporadic. The first Penelope element was identified in Drosophila virilis, where it was shown to participate in hybrid dysgenesis [3,4]. Its structural and functional properties are those of a typical retrotransposon, consisting of a single open reading frame (ORF). This ORF encodes a reverse transcriptase (RT) domain responsible for RNA-templated DNA synthesis, and an endonuclease (EN) domain responsible for integration of a reverse-transcribed cDNA copy into new chromosomal locations, generating short target site duplications (TSD) upon insertion. The EN domain associated with PLEs belongs to endonucleases of the GIY-YIG superfamily, which were originally identified in group I mobile introns from bacteria and organelles [5-8]. The Penelope EN domain was overexpressed in E. coli and shown to possess DNA cleavage activity, while the baculovirus-expressed RT was capable of RNA-dependent DNA synthesis in vitro[9].

In addition to EN-containing PLEs, there is a distinct PLE subclass which lacks the EN domain altogether [10]. Such EN-deficient PLEs are apparently able to prime DNA synthesis from the 3′ ends of the exposed chromosome termini, either at deprotected telomeres or at sites of double-strand DNA breakage, thereby obviating the need for endonuclease activity. Accordingly, their transposition is largely confined to chromosome ends, where it is followed by the addition of telomeric repeats to the truncated 5′ end of the element. Such EN-deficient PLEs are found in selected animal, fungal, protist and plant species, but their distribution is highly sporadic.

Rotifers of the class Bdelloidea, in which EN-deficient PLEs were discovered, are microscopic freshwater invertebrates that reproduce asexually, can survive frequent rounds of desiccation and rehydration, and contain significant amounts of horizontally transferred genes in their genomes [11-13]. The high-quality draft genome sequence of the first representative of the phylum Rotifera, the bdelloid Adineta vaga, was recently completed [14]. Only about 3% of its genomic DNA is represented by transposable elements (TEs), and while the diversity of families is high, each family contains very few members, indicating that incoming TEs do not proliferate efficiently in the A. vaga genome. While PLEs make up almost one-third of all A. vaga retroelements (a total of 24 families, occupying approximately 0.74 Mb of the 218-Mb assembly), the majority of the A. vaga PLEs are represented by EN-deficient Athena retroelements [10]. Here we report that the A. vaga genome also contains a small number of “canonical” Penelope elements with the GIY-YIG endonuclease domain, which, however, exhibit several highly unusual features.

Results

Identification and phylogenetic analysis of A. vaga Penelope families

We performed an exhaustive search of the A. vaga genome assembly, aiming at identification of every Penelope copy in the assembly and reconstruction of their complete genomic evolutionary history. Additional file 1: Table S1 lists all of the full-length and partial copies, as well as their coordinates in the assembly. A total of 36 copies spanning a sufficiently long stretch (at least one-third) of the coding sequence to be included into phylogenetic analysis were aligned, and their phylogenetic relationships were determined in order to place their structural and functional properties into phylogenetic context (Figure 1). The corresponding alignment of Penelope coding sequences is provided in the Additional file 2: Data file 1. Based on their structural organization and the degree of protein sequence similarity, all Penelope retrotransposons in A. vaga could be divided into six major groups (Pen1-Pen6_Av) and further into 11 families (1a, 2b and so on), with each family represented by very few copies (Figure 1, Additional file 1: Table S1).

Additional file 1: Table S1. Inventory of the A. vaga Penelope full-length copies and fragments in the assembled scaffolds.

Format: XLSX Size: 30KB Download fileOpen Data

thumbnailFigure 1. Maximum likelihood analysis ofA. vaga Penelopenucleotide sequences. Branch support is indicated at the nodes. Penelope insertions localized in collinear allelic pairs are shaded. Intact copies are boxed. Brackets designated N1-N4 denote the presence of different N-rich inserts in each group of elements, as described in the text. Scale bar, nucleotide substitutions per site.

Additional file 2. Nucleotide sequence alignment of A. vaga Penelope coding sequences shown in Figure 1.

Format: FAS Size: 232KB Download fileOpen Data

The evolutionary history of Penelope retrotransposons in the sequenced A. vaga isolate reveals that all copies are arranged in two major branches, consisting of Pen1-2_Av and Pen3-6_Av elements, respectively. High support values for the majority of nodes are indicative of relatively few insertion events that gave rise to extant copies. Overall, 6 out of 37 ORFs presented in Figure 1 appear intact (boxed), although intactness is not associated with a higher degree of proliferation in the genome. The majority of copies contain defects in their ORFs, such as frameshifts, in-frame stop codons, indels or truncations.

Structural organization of Penelope families

The typical Penelope structure, also observed in other animals, such as fruit flies and fish [3,15,16], is exemplified by a single-copy element Pen2a_Av appearing as a secondary insertion into Pen3 on scaffold 671 in the opposite orientation (Figure 2a). Its 842-aa ORF, with an in-frame stop codon, is bounded by two 218-base pairs (bp) “pseudo-long terminal repeats” (pLTRs) [15,16], and an adjacent inverted pLTR completes the entire insert, which in this case is flanked by a 9-bp TSD. Also found is the characteristic 31-bp extension, or “tail”, which is optionally present at the 3′ end of one of the inverted pLTRs [16]. The pLTR includes the first 12 amino acids (aa) of the ORF, and together with the tail, this length can be extended to 22 amino acids. The inverted pLTR at the 5′ end overlaps the direct pLTR by 15 bp, and is 37-bp shorter than the two full pLTRs (181 bp). The pLTR contains a putative TATA box (TATATATA) separated by 20 bp from an initiator-(Inr)-like sequence (TCACT), and could, therefore, exhibit basal promoter activity. It is worth noting that this TATA sequence can be read in both directions, and the opposite direction also features a downstream Inr-like sequence ACATT, raising the possibility of a bidirectional promoter. Pen2a_Av occurs in the assembly only once, and has not given rise to any new copies or fragments. Similar pLTR structures are also found in most of the families described below.

thumbnailFigure 2. Structural features of selectedA. vaga Peneloperetrotransposons. ORFs are represented by colored boxes with arrows. RT, reverse transcriptase; EN, endonuclease. Thin arrows denote pLTRs, and small colored rectangles - its optional short extension (“tail”). Panels (a-i) correspond to different families. Thicker arrows represent repeats derived from sequences other than pLTRs. N1 to N3 denote different N-rich inserts within ORFs, shown by darker colors. Palindromes are shown by double lines; frameshifts or stop codons, by vertical lines; deletions, by dashed lines; gaps, by dotted lines. Numbers above small yellow boxes indicate the length of target site duplications in bp. Scale bar, 1 kb.

For Pen2_Av, the only intact and potentially active ORF (838 aa) is present on scaffold 878 (Figure 2b). This element consists of two copies, one full-length and one 5′-truncated, which are arranged in a partial tandem and inserted into a single-copy non-LTR retrotransposon. Such partial tandems can be transpositionally active, as was demonstrated by the successful introduction of a similarly structured Penelope copy from D. virilis into D. melanogaster[17]. Since the structure of another non-LTR retrotransposon closely related to the Pen2 target (76% identity) was already known, it was possible to determine that the Pen2 insertion in this case did not cause a TSD, but instead formed its 5′ junction via microhomology-mediated annealing, as was described for long interspersed elements (LINEs) [18]. Its 193-bp pLTR contains an 18-bp palindrome at the 5′ end. This copy may also have given rise to another insertion on scaffold 304 organized in a way identical to Pen2a, that is, flanked by inverted pLTRs with a 10-bp TSD (Figure 2c). This incomplete derivative contains an internal microhomology-mediated deletion and an in-frame stop codon. A related Pen2 subfamily consists of two 5′-truncated members, with the longest one containing an in-frame stop codon and flanked by inverted 212-bp pLTRs, but no TSD.

Pen1_Av elements exhibit a similar overall structure to Pen2_Av, except that, in most cases, pLTRs are present in direct orientation only. Unexpectedly, the 3′-terminal pLTR in Pen1 is separated from the rest of the element by a long unique spacer varying between 0.9 and 1.5 kb in length (Figure 2e, f). Apparently, the spacer is formed via capture of host DNA, as copies that are 90% identical in sequence exhibit no detectable nucleotide sequence similarity between spacers. This family contains the largest number of apparently intact copies: three out of four members code for an 830-aa ORF preserving all of the functionally conserved characteristic RT and EN motifs.

Pen5_Av and Pen6_Av elements are transpositionally inactive, as even their longest representatives contain internal deletions, in-frame stop codons or 5′-truncations. In two cases, ancestral Pen5 and Pen6 insertions apparently became fixed as two allelic versions: these 5′-truncated copies are surrounded by the same host genes with an overall 5% sequence divergence across the entire locus (Figure 1). A similar pattern is seen for two allelic versions of a highly decayed Pen1 copy on scaffolds 19 and 160. Pen5_Av and Pen6_Av are bounded by inverted pLTRs; however, their exact boundaries are more difficult to determine because of possible decay. Interestingly, despite the presence of two stop codons and a frameshift, a divergent Pen5 copy is actively transcribed, as evidenced by RNA-seq data (see below, Figure 3a), and contains a spliceosomal intron within the ORF.

thumbnailFigure 3. Transcription and RNA-mediated silencing ofA. vaga Penelopefamilies. (a) RNA-seq counts per family. Numbers on the Y axis represent RNA-seq counts per kb, and the moderately transcribed A. vaga Dicer-like genes [14] are used for comparison. Transcripts originating from the N2-related segment on scaffold 412 (see text) could not be accommodated using the same scale. (b-e) Small RNA coverage plots along selected full-length Penelope copies shown in Figure 2. X axis, element length in bp; Y axis, small RNA counts per window of indicated size; red, sense reads; blue, antisense reads. (f) Coverage plot for scaffold 412; Pen3A pLTR is in the opposite orientation to the transcribed N2-related segment.

Asparagine-rich insertions in Penelope coding sequences

An early-branching lineage of Pen2a, represented by two copies in the assembly, contains a lengthy 1.5-kb insertion (N1) into its coding region between the RT and EN domains (Figures 1 and 2d). The inserted fragment is exceptionally rich in asparagine (N) residues (approximately 30%), but nevertheless it does not interrupt the ORF on scaffold 942, resulting in a 1,309-aa coding sequence. Part of the N-rich insert (304 bp) is also found upstream of the 5′ pLTR in inverted orientation (Figure 2d).

Analogous structural variations were observed in Pen3 and Pen4 families, albeit in a different relative position - between the core RT and the thumb domain (Figure 2g-i). Due to the tendency to form long tandem/inverted repeat structures, none of these elements could be initially assembled in its entirety, with the exception of one copy on scaffold 607 containing an in-frame stop codon (Figure 2g). Two Pen3 copies were located on detached contigs containing permuted overlapping 5′- and 3′-terminal parts of the element, in inverted orientation. In these cases, the original structure was inferred by reconstituting the entire ORF from its overlapping N- and C-terminal halves, so that it would be similar in structure to the copy shown in Figure 2g. However, such structures cannot be dismissed as assembly artifacts, because small RNA profiles (see below) switch polarity between the two halves. All Pen3 and Pen4 elements carry an insertion of different N-rich segments (N2 to N4) into an ancestral copy resembling a single-copy intact Pen3a, which has no such insertions (Figure 1, Figure 2i). There were at least three independent occurrences of long N-rich insertions into the same relative position of Pen3/Pen4, with the length of inserted segments varying between 460 and 554 aa, all of them having an asparagine content of 25 to 30%. Overall, it appears that N-rich insertions tend to arise in ORF regions that were initially enriched in short (AAY)n motifs.

Transcription and RNA-mediated silencing

We sought to determine the possible origin of the N-rich segments inserted into Penelope ORF. While the 1.5-kb segments in Pen2a could not be found elsewhere in the assembly without being connected to Penelope ORF, a 1-kb region of homology 85% identical to the N-rich segment from Pen3 was found near a Pen3 solo pLTR on scaffold 412, and, moreover, it was highly transcribed on its own, but yielded a very poor antisense small RNA signal (Figure 3a, f). In contrast, transcription from most individual Penelope families was more than an order of magnitude lower, and was comparable in intensity to weakly transcribed A. vaga genes, such as Dicer endonuclease homologs [14] (Figure 3a). Families without full-length copies, such as Pen3b and Pen4, yielded very low transcript levels close to background, while Pen5 yielded higher transcript levels and low antisense small RNA coverage (Figure 3e). Overall, most Penelope families exhibit relatively low RNA-seq coverage and high steady-state levels of endogenous small RNA coverage predominantly in antisense orientation, indicating efficient operation of RNA-mediated silencing mechanisms directed against their activity (Figure 3).

Role of Penelope in host gene expansion

The single-copy Pen3a_Av (Figure 2i), which may have lost its mobility due to a pogo transposon insertion at the very end of the 3′ pLTR, may have participated in retrotransposon-mediated host gene family expansion. Its ORF apparently acted in trans to yield an integration event in which a gene coding for a non-ribosomal peptide synthetase (NRPS), initially of bacterial origin, was copied into a new chromosomal location (Figure 4). This NRPS gene has preserved all of its introns, which are present in other members of this multigene family (totaling about 50 copies per genome). It is flanked by two direct and one inverted pLTR in an arrangement similar to that depicted in Figure 2a, and by an 8-bp TSD. The pLTR of Pen3a has a nearly-perfect 38-bp palindrome at its 5′ end. The NRPS ORF is located between the two direct pLTRs, but there are no internal sequences in common with Pen3a, indicating that the cis-acting pLTR sequences were sufficient to provide integration of the entire structure in trans. We also found a few other cases in which unrelated sequences were captured between solo pLTRs and surrounded by TSDs, although those sequences did not code for proteins. In addition, a more ancient Pen3-mediated event may have resulted in transposition of another multigene family member encoding a leucine-rich repeat (LRR) protein: it is present on two allelic scaffolds (875 and 956), with each allele containing the same pLTR to the 3′ end of the LRR gene. Several solo pLTRs were not associated with any other Penelope sequences or TSDs, indicating that recombination and/or deletion of surrounding sequences may have played a role in their formation.

thumbnailFigure 4. Penelope-mediated mobilization of an intron-containing NRPS gene. Shown are the two scaffolds which constitute an allelic pair containing glucose-6-phosphate isomerase (G6PI) and RXR-like retinoic acid receptor (RXR) coding sequences. Scaffold 385 harbors a NRPS insertion flanked by Pen3a pLTRs (see Figure 2i) and by an 8-bp target site duplication (GAATTAAT), which is present only once on scaffold 561. Introns are denoted by V-shaped lines; other features are as in Figure 2. Scale bar, 1 kb.

To verify that the pLTR-NRPS combination indeed originated as a result of transposition, rather than a recombinational event bringing together two pLTRs with the same adjacent 8-bp sequence by chance, we searched the assembly for the putative “empty site”. Indeed, we found that scaffold 385 has an allelic partner, scaffold 561, containing the same genes (glucose-6-phosphate isomerase and retinoic acid receptor RXR-alpha) with an overall nucleotide sequence divergence of 2% (Figure 4). As expected, the 8-bp TSD is present on scaffold 561 only once, providing direct evidence that it was indeed duplicated upon insertion of the entire pLTR-NRPS structure.

Phylogenetic placement of A. vaga Penelope families

Comparison of A. vaga Penelope retrotransposons with PLEs from other taxa shows that they are most closely related to the flatworm Perere clade containing Perere10 from Schistosoma mansoni, S. japonicum and Schmidtea mediterranea[19,20]. The two A. vaga Penelope branches are about as distant from each other as they are from the flatworm Perere10 elements (Figure 5). They are clearly grouped with other retrotransposons of the Penelope/Poseidon group, as opposed to Neptune-like retrotransposons, which have a cysteine-rich domain between RT and EN [20]. In this respect, it is worth mentioning that Pen3_Av and Pen5a_Av families contain a short Cys-rich insert in a different location, between the RT core motifs 3 and 4 (Cys/His-X1-3-Cys-X10-Cys-X2-Cys). Its significance, however, remains obscure. Most PLEs that can be found in early genomic drafts of two species of monogonont rotifers, Brachionus manjavacas and B. calyciflorus, are closely related to the Neptune group (Figure 5) and contain the characteristic cysteine-rich domain between RT and EN [20]. In agreement with our earlier findings [10], the most abundant type of A. vaga PLEs, the telomere-associated EN-deficient Athena retroelements, constitute a distinct clade, as do the EN-deficient PLEs from fungi and protists. It should be kept in mind that the current phylogeny includes only the extant A. vaga families, as this species keeps very little “fossil record” of TEs due to actively ongoing deletion and high TE turnover rate as a consequence of desiccation-induced DNA repair and, therefore, any ancestral evolutionary intermediates are likely to have been eliminated from the genome.

thumbnailFigure 5. Phylogenetic relationships of EN-containing and EN-deficient PLEs. Clade markers are as follows: Perere in flatworms and A. vaga, magenta diamonds; Penelope/Poseidon, cyan triangles; Neptune, blue circles; Nematis, gray triangles; EN-deficient Athena, green squares; EN-deficient protist and fungal PLEs, brown squares. Most taxon designations are from datasets in [10,20]; Bman, Brachionus manjavacas; Bcal, Brachionus calyciflorus; EN, endonuclease; PLEs, Penelope-like elements. Branch support values over 60% are shown. Scale bar, amino acid substitutions per site.

Discussion

Completion of the high-quality draft genome sequence of a bdelloid rotifer, Adineta vaga, provides us with an opportunity to investigate the entire TE complement in a long-term asexual species, and to obtain a comprehensive picture of genome-wide TE distribution and evolutionary history. This study is focused on PLEs, an enigmatic class of retroelements which include EN-containing retrotransposons from numerous animal genomes, as well as telomere-associated EN-deficient retroelements from rotifers, fungi, protists and plants [10,16,20]. While we observe co-existence, within the genome of the same species, between the conventional Penelope retrotransposons with the GIY-YIG EN domain and the EN-deficient PLEs, as was recently reported in the kuruma shrimp [21], there is no indication of cross-mobilization of EN-deficient Athena elements by the Penelope-encoded EN. For each A. vaga Penelope family, its mobility in the genome apparently relies on the presence of element-specific terminal structures required for retrotransposition, termed pLTRs, which do not exhibit any association with Athena elements. It should be noted that fungal genomes contain only EN-deficient PLEs and no EN-containing ones, again indicating that the maintenance of the former does not depend on the latter.

The present analysis of Penelope retrotransposons in A. vaga, while illustrating their overall similarity to Penelope elements in other species, including the extreme structural variability, also highlights their peculiar features that may contribute to the evolutionary plasticity of the bdelloid genome characterized by high levels of gene conversion, by relatively low but highly diversified TE content, and by the presence of numerous genes of foreign origin and substantial lineage-specific expansions of various multigene families [14]. Expansions involve gene families, including NRPS and other foreign genes, as well as 7-transmembrane receptors and proteins containing repeated motifs, such as LRR, TPR, PPR, Kelch, NHL, FG-GAP and so on. Paradoxically, many gene families are amplified to a much higher copy number than TE families. These multigene families are likely involved in processes that involve diversification of gene function, such as host defense and immunity, production of secondary metabolites, chemosensory perception, extracellular signaling and cell-cell communication.

We find that A. vaga Penelope elements can mobilize host genes surrounded by terminal pLTR structures and, therefore, can contribute to observed lineage-specific expansions of certain gene families, shedding light on some of the mechanisms that multiply host genes to copy numbers higher than most TEs. While other TE classes also have the potential to contribute to amplification of gene families, which could then be followed by their diversification, Penelope elements have a distinct advantage over other retrotransposons in this respect, as their retrotransposition mechanism apparently allows intron retention [1]. Our analysis reveals no strong evidence that any intact A. vaga Penelope ORFs were exapted as domesticated genes, as none of them are present on two collinear allelic chromosome segments. Those Penelope fragments that we do find in collinear pairs are badly damaged, and their function, if any, would not involve Penelope-encoded products. The most likely agents involved in gene amplification are the Penelope families with the capacity to incorporate relatively long stretches of host DNA between pLTRs, such as Pen1_Av and Pen3a_Av. Four out of six apparently intact Penelope ORFs belong to these families. While the propensity of A. vaga for DNA deletion could rapidly erase one or both pLTRs from the genome, making it difficult to detect additional cases of pLTR-mediated gene amplification, the example described here leaves little doubt that such events can indeed contribute to lineage-specific expansion of multigene families.

Even though the overall TE content in A. vaga is quite low by metazoan standards, the particularly low Penelope copy number in comparison to other retrotransposons is striking. While some TEs could remain undetected in a de novo assembly consisting of over 30,000 scaffolds with N50 of 260 kb [14], there is little reason to believe that most Penelope copies would be preferentially undetectable. Two circularly permuted copies located on isolated contigs with little or no flanking sequences may represent active elements which could not be properly assembled due to the fusion of several identical copies into a single contig. Although studies of PLE distribution along the chromosome length will have to await chromosome-sized scaffolds, the majority of Penelope copies are present on relatively small scaffolds (Additional file 1: Table S1), and inspection of their genomic environment shows that they are largely compartmentalized in TE-rich regions, which may represent non-essential genomic islands consisting of various TEs, genes of foreign origin and members of diverse multigene families.

Like all other TEs in the genome, Penelopes are subject to the generalized host defense responses, such as RNA-mediated silencing. Indeed, we find that most of the A. vaga Penelope copies give rise to small RNAs with preferential antisense polarity. The Penelope element in Drosophila was previously shown to elicit small RNA response after invasion [22,23]. We also observed that many Penelope copies were disabled by microhomology-mediated deletions, a mechanism of TE inactivation that is applicable to most other TEs and likely operates during DNA repair following frequent cycles of desiccation and rehydration [14,24]. However, Penelope elements constitute only about 2% of A. vaga TEs, and only 4% of its retroelements. Thus, additional family-specific mechanisms should be invoked to explain their much lower relative abundance in comparison with other TEs. Most likely, their low proliferation capacity may be associated with peculiarities of their replication mechanism in this species.

A previously undescribed phenomenon is the appearance of very long inserts in the coding regions of Pen2-Pen5 elements, which do not necessarily disrupt ORF integrity and are highly enriched in asparagine residues. It appears that copies with such inserts would still be capable of retrotransposition, although their ORFs would be increased in size from the usual 800 to 900 to 1,300 to 1,500 aa, and the domain structure perturbed. For Pen2a, the inserted segment could serve as a long linker between the RT and EN domains, while in Pen3 to 4 such a linker would connect the core RT with its thumb domain. Analogous inserts have not been previously observed in other TEs, and it is reasonable to suggest that they arise as a consequence of the complicated molecular gymnastics that PLEs perform during their replication. In particular, the existence of an autonomous highly transcribed N-rich segment in the vicinity of Pen3a pLTR indicates that it could have been captured in trans and internalized. We also noticed that in the candidate precursor elements, such as Pen2 and Pen3a, regions roughly corresponding to the linker insertion sites in Pen2a and Pen3 to 4 contain several short stretches of asparagine residues. In addition, a secondary insertion of Pen2a into Pen3 on scaffold 671 also occurred into the N-rich segment, indicating that this sequence may serve as an attractive target for Penelope insertions. Since Penelope elements were previously reported to favor simple AT-rich sequences as preferred targets [16], we propose that such inserts may arise as a result of spurious self-priming by read-through transcripts containing the adjacent flanks enriched in simple trinucleotide repeats, followed by template jumps. In such cases, the short internal stretches of the N-rich coding sequence (AAT)n or (AAC)n could help in keeping the reading frame of the inserted segment properly aligned, and a chimeric ORF could persist in the genome if it codes for an uninterrupted polypeptide.

The propensity of Penelope elements for self-priming may be inferred from the abundance of inverted-repeat structures containing palindromes at the inverted junction, as shown in Figure 2. Consistent occurrence of such palindromes is best interpreted in terms of self-priming, which, however, would have to occur on an antisense template (if a sense template is used, self-priming at the 3′ end would result in a tail-to-tail inverted repeat arrangement, as opposed to the most frequently observed head-to-head). Moreover, utilization of an antisense template is highly compatible with intron retention, since introns would not be recognized in an antisense orientation by the splicing machinery. The presence of oppositely oriented promoter motifs in pLTRs also argues in favor of bidirectional PLE transcription. However, we cannot currently exclude the possibility of utilization of an unspliced sense transcript as a template, and further experiments will be required to discriminate between these possibilities. Direct demonstration of antisense promoter activity in Penelope elements and full elucidation of its replication cycle constitutes a promising subject for future studies.

Conclusions

Penelope elements occupy a special place among TE superfamilies because of their variable structure representing a flexible arrangement of direct and/or inverted repeats. This structure exhibits a high degree of conservation among all animals harboring EN-containing PLEs, while the protist and fungal genomes contain only EN-deficient PLEs, which do not share this structural organization. Our analysis reveals co-existence of two distinct PLE types within the genome of the same host species with no evidence of cross-mobilization between families, indicating that the element-encoded enzymatic activities and its cis-acting sequences are co-adapted. The EN-containing PLEs were shown to participate in expansion of intron-containing multigene families in the host. We also describe a new phenomenon of insertion of long N-rich segments into the coding sequence, not previously observed in other retroelements, and hypothesize that it may occur as a consequence of the atypical replication mechanism. Taking all of the observed structural features into consideration, we hypothesize that EN-containing PLEs use a self-priming mechanism of replication, which would result in intron retention if it utilizes an antisense template. However, further experiments are required to discriminate between possible alternative models.

Methods

Initial PLE identification in A. vaga was done in the course of genome analysis as described in [14], with relatively low recovery from REPET and ReAS pipelines due to the low copy number, which hampers identification of numerous single-copy elements. Additional BLAST searches were performed using the conserved GIY-YIG and RT domains as queries, and after identification and boundary adjustment of full-length copies, these were used as queries to identify shorter fragments using BLAT [25]. Multiple sequence alignment was done with MUSCLE [26]. A. vaga Penelope sequences were aligned as amino acids in MEGA v.5.10 [27] and untranslated back into nucleotides. Maximum likelihood analysis of nucleotide sequences was performed with RAxML [28]. For comparison with PLEs from other species, the initial datasets from [20] and [10] were supplemented with PLEs characterized in the present study, and neighbor-joining and minimum evolution analyses of protein-coding sequences were performed in MEGA (Poisson model, gamma distributed rates among sites, 1,000 bootstrap replications). RNA-seq counts were determined with the aid of a custom Ruby script available upon request. DNA and RNA sequencing data were generated by the A. vaga sequencing consortium, and all of the scaffold numbers and coordinates correspond to the assembly in [14]. Validation of selected sequences and closure of gaps in genomic DNA was done by PCR using custom oligonucleotide primers available upon request. Detailed procedures for small RNA isolation and analysis will be published elsewhere (Rodriguez and Arkhipova, in preparation). Briefly, HiTrap Q (GE Healthcare Life Sciences, Pittsburgh, PA, USA) column chromatography eluates corresponding to protein-bound fractions from A. vaga lysates were collected to extract endogenous small RNAs as described in [29]. This protocol results in preferential extraction of small RNAs bound to Argonaute/Piwi proteins, and over 80% of the obtained reads correspond to the piRNA-like category 25 to 32 nt in length with a strong 5′-uridine bias. A small RNA library was processed for sequencing on the Illumina HiSeq platform. After initial filtering, small RNAs were mapped using Bowtie [30] to the individual A. vaga Penelope sequences. Coverage plots along each element were produced with custom C and R scripts.

Abbreviations

bp: Base pair(s); EN: Endonuclease; Inr: Initiator; LRR: Leucine-rich repeat; NRPS: Non-ribosomal peptide synthetase; ORF: Open reading frame; pLTR: Pseudo-LTR; PLE: Penelope-like element; PCR: Polymerase chain reaction; RT: Reverse transcriptase; TE: Transposable element; TSD: Target site duplication.

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

IA designed the study, performed data analysis and wrote the manuscript. IY compiled the TE inventory, analyzed transcription data, validated genomic sequences by PCR and closed the sequence gaps. FR constructed small RNA libraries and participated in data analysis. All authors read and approved the final manuscript.

Acknowledgements

We are thankful to D. Mark Welch for providing access to the draft genome sequences of B. manjavacas and B. calyciflorus, to D. Mozzherin for help with the RNA-seq script, to N. Lau and G. Chirn for sharing their coverage plot scripts, and to anonymous reviewers for constructive comments. This research was supported by grants MCB-0821956 and MCB-1121334 from the U.S. National Science Foundation to I.A.

References

  1. Arkhipova IR, Pyatkov KI, Meselson M, Evgen’ev MB: Retroelements containing introns in diverse invertebrate taxa.

    Nat Genet 2003, 33:123-124. PubMed Abstract | Publisher Full Text OpenURL

  2. Arkhipova IR: Telomerase, retrotransposons, and evolution. In Telomerases: Chemistry, Biology and Clinical Applications. Edited by Lue NF, Autexier C. Hoboken, NJ: John Wiley and Sons, Inc; 2012:265-299. OpenURL

  3. Evgen’ev MB, Zelentsova H, Shostak N, Kozitsina M, Barskyi V, Lankenau DH, Corces VG: Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis.

    Proc Natl Acad Sci USA 1997, 94:196-201. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  4. Vieira J, Vieira CP, Hartl DL, Lozovskaya ER: Factors contributing to the hybrid dysgenesis syndrome in Drosophila virilis.

    Genet Res 1998, 71:109-117. PubMed Abstract | Publisher Full Text OpenURL

  5. Lyozin GT, Makarova KS, Velikodvorskaja VV, Zelentsova HS, Khechumian RR, Kidwell MG, Koonin EV, Evgen’ev MB: The structure and evolution of Penelope in the virilis species group of Drosophila: an ancient lineage of retroelements.

    J Mol Evol 2001, 52:445-456. PubMed Abstract | Publisher Full Text OpenURL

  6. Volff JN, Hornung U, Schartl M: Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements.

    Mol Genet Genomics 2001, 265:711-720. PubMed Abstract | Publisher Full Text OpenURL

  7. Belfort M, Roberts RJ: Homing endonucleases: keeping the house in order.

    Nucleic Acids Res 1997, 25:3379-3388. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  8. Dunin-Horkawicz S, Feder M, Bujnicki JM: Phylogenomic analysis of the GIY-YIG nuclease superfamily.

    BMC Genomics 2006, 7:98. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  9. Pyatkov KI, Arkhipova IR, Malkova NV, Finnegan DJ, Evgen’ev MB: Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.

    Proc Natl Acad Sci USA 2004, 101:14719-14724. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  10. Gladyshev EA, Arkhipova IR: Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes.

    Proc Natl Acad Sci USA 2007, 104:9352-9357. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  11. Mark Welch D, Meselson M: Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange.

    Science 2000, 288:1211-1215. PubMed Abstract | Publisher Full Text OpenURL

  12. Ricci C: Anhydrobiotic capabilities of bdelloid rotifers.

    Hydrobiologia 1998, 387–388:321-326. OpenURL

  13. Gladyshev EA, Meselson M, Arkhipova IR: Massive horizontal gene transfer in bdelloid rotifers.

    Science 2008, 320:1210-1213. PubMed Abstract | Publisher Full Text OpenURL

  14. Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin E, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthelemy R, Bast J, Bazykin G, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatchek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan J, Vakhrusheva O, Wajnberg E, et al.: Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

    Nature 2013, 500:453-457. PubMed Abstract | Publisher Full Text OpenURL

  15. Dalle Nogare DE, Clark MS, Elgar G, Frame IG, Poulter RT: Xena, a full-length basal retroelement from tetraodontid fish.

    Mol Biol Evol 2002, 19:247-255. PubMed Abstract | Publisher Full Text OpenURL

  16. Evgen’ev MB, Arkhipova IR: Penelope-like elements–a new class of retroelements: distribution, function and possible evolutionary significance.

    Cytogenet Genome Res 2005, 110:510-521. PubMed Abstract | Publisher Full Text OpenURL

  17. Pyatkov KI, Shostak NG, Zelentsova ES, Lyozin GT, Melekhin MI, Finnegan DJ, Kidwell MG, Evgen’ev MB: Penelope retroelements from Drosophila virilis are active after transformation of Drosophila melanogaster.

    Proc Natl Acad Sci USA 2002, 99:16150-16155. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  18. Zingler N, Willhoeft U, Brose HP, Schoder V, Jahns T, Hanschmann KM, Morrish TA, Löwer J, Schumann GG: Analysis of 5′ junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5′-end attachment requiring microhomology-mediated end-joining.

    Genome Res 2005, 15:780-789. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  19. DeMarco R, Machado AA, Bisson-Filho AW, Verjovski-Almeida S: Identification of 18 new transcribed retrotransposons in Schistosoma mansoni.

    Biochem Biophys Res Commun 2005, 333:230-240. PubMed Abstract | Publisher Full Text OpenURL

  20. Arkhipova IR: Distribution and phylogeny of Penelope-like elements in eukaryotes.

    Syst Biol 2006, 55:875-885. PubMed Abstract | Publisher Full Text OpenURL

  21. Koyama T, Kondo H, Aoki T, Hirono I: Identification of two Penelope-like elements with different structures and chromosome localization in kuruma shrimp genome.

    Mar Biotechnol (NY) 2013, 15:115-123. Publisher Full Text OpenURL

  22. Blumenstiel JP, Hartl DL: Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis.

    Proc Natl Acad Sci USA 2005, 102:15965-15970. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  23. Rozhkov NV, Aravin AA, Zelentsova ES, Schostak NG, Sachidanandam R, McCombie WR, Hannon GJ, Evgen’ev MB: Small RNA-based silencing strategies for transposons in the process of invading Drosophila species.

    RNA 2010, 16:1634-1645. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  24. Gladyshev EA, Arkhipova IR: A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5′ truncations.

    Mob DNA 2010, 1:12. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  25. Kent WJ: BLAT - the BLAST-like alignment tool.

    Genome Res 2002, 12:656-664. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  26. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput.

    Nucleic Acids Res 2004, 32:1792-1797. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

    Mol Biol Evol 2011, 28:2731-2739. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  28. Stamatakis A, Hoover P, Rougemont J: A rapid bootstrap algorithm for the RAxML web-servers.

    Syst Biol 2008, 75:758-771. OpenURL

  29. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE: Characterization of the piRNA complex from rat testes.

    Science 2006, 313:363-367. PubMed Abstract | Publisher Full Text OpenURL

  30. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

    Genome Biol 2009, 10:R25. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL