The first non-LTR retrotransposon characterised in the cephalochordate amphioxus, BfCR1, shows similarities to CR1-like elements

APE-type non-LTR retrotransposons of multicellular organisms encode virus-like 2A oligopeptide sequences, which mediate translational recoding during protein synthesis

2A oligopeptide sequences (“2As”) mediate a cotranslational recoding event termed “ribosome skipping.” Previously we demonstrated the activity of 2As (and “2A-like sequences”) within a wide range of animal RNA virus genomes and non-long terminal repeat retrotransposons (non-LTRs) in the genomes of the unicellular organisms Trypanosoma brucei (Ingi) and T. cruzi (L1Tc). Here, we report the presence of 2A-like sequences in the genomes of a wide range of multicellular organisms and, as in the trypanosome genomes, within non-LTR retrotransposons (non-LTRs)—clustering in the Rex1, Crack, L2, L2A, and CR1 clades, in addition to Ingi. These 2A-like sequences were tested for translational recoding activity, and highly active sequences were found within the Rex1, L2, CR1, and Ingi clades. The presence of 2A-like sequences within non-LTRs may not only represent a method of controlling protein biogenesis but also shows some correlation with such apurinic/apyrimidinic DNA endonuclease-type non-LTRs encoding one, rather than two, open reading frames (ORFs). Interestingly, such non-LTRs cluster with closely related elements lacking 2A-like recoding elements but retaining ORF1. Taken together, these observations suggest that acquisition of 2A-like translational recoding sequences may have played a role in the evolution of these elements.

DNA methylation in amphioxus: from ancestral functions to new roles in vertebrates

In vertebrates, DNA methylation is an epigenetic mechanism that modulates gene transcription, and plays crucial roles during development, cell fate maintenance, germ cell pluripotency and inheritable genome imprinting. DNA methylation might also play a role as a genome defense mechanism against the mutational activity derived from transposon mobility. In contrast to the heavily methylated genomes in vertebrates, most genomes in invertebrates are poorly or just moderately methylated, and the function of DNA methylation remains unclear. Here, we review the DNA methylation system in the cephalochordate amphioxus, which belongs to the most basally divergent group of our own phylum, the chordates. First, surveys of the amphioxus genome database reveal the presence of the DNA methylation machinery, DNA methyltransferases and methyl-CpG-binding domain proteins. Second, comparative genomics and analyses of conserved synteny between amphioxus and vertebrates provide robust evidence that the DNA methylation machinery of amphioxus represents the ancestral toolkit of chordates, and that its expansion in vertebrates was originated by the two rounds of whole-genome duplication that occurred in stem vertebrates. Third, in silico analysis of CpGo/e ratios throughout the amphioxus genome suggests a bimodal distribution of DNA methylation, consistent with a mosaic pattern comprising domains of methylated DNA interspersed with domains of unmethylated DNA, similar to the situation described in ascidians, but radically different to the globally methylated vertebrate genomes. Finally, we discuss potential roles of the DNA methylation system in amphioxus in the context of chordate genome evolution and the origin of vertebrates.

Evolution of serum albumin intron-1 is shaped by a 5' truncated non-long terminal repeat retrotransposon in western Palearctic water frogs (Neobatrachia)

A 5' truncated non-LTR CR1-like retrotransposon, named RanaCR1, was identified in the serum albumin intron-1 (SAI-1) of at least seven species of western Palearctic water frogs (WPWF). Based on sequence similarity of the carboxy-terminal region (CTR) of ORF2 and/or the highly conserved 3' untranslated region (3' UTR), RanaCR1-like elements occur also in the genome of Xenopus tropicalis and Rana temporaria. Unlike other CR1 elements, RanaCR1 contains a CA microsatellite in its 3' UTR. The low nucleotide diversity of the 3' UTR compared to the CTR and to SAI-1 suggests that this region still plays a role in WPWF, either as a structure-stabilizing element, or within a species-specific transcriptional network. Length variation of water frog SAI-1 sequences is caused by deletions that extend in some cases beyond the 5' or 3' ends of RanaCR1, probably a result of selection for structural and functional stability of the primary transcript. The impact of RanaCR1 on SAI-1 evolution is also indicated by the significant negative correlation between the length of both SAI-1 and RanaCR1 and the percentage GC content of RanaCR1. Both SAI-1 and RanaCR1 sequences support the sister group relationship of R. perezi and R. saharica, which are placed in the phylogenetic tree at a basal position, the sister clade to other water frog taxa. It also supports the monophyly of the R. lessonae group; of Anatolian water frogs (R. cf. bedriagae), which are not conspecific with R. bedriagae, and of the European ridibunda group. Within the ridibunda clade, Greek frogs are clearly separated, supporting the hypothesis that Balkan water frogs represent a distinct species. Frogs from Atyrau (Kazakhstan), the type locality of R. ridibunda, were heterozygous for a ridibunda and a cf. bedriagae specific allele.

Specific chicken repeat 1 (CR1) retrotransposon insertion suggests phylogenetic affinity of rockfowls (genus Picathartes) to crows and ravens (Corvidae)

While the monophyly of the order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, both on morphological and molecular grounds, lower phylogenetic relationships have been a continuous matter of debate, especially within oscines. This is particularly true for the rockfowls (genus Picathartes), which phylogenetic classification has been an ongoing puzzle. Sequence-based molecular studies failed in deriving unambiguously resolved and supported hypotheses. We present here a novel approach: use of retrotransposon insertions as phylogenetic markers in passerine birds. Chicken repeat 1 (CR1) is the most important non-LTR retrotransposon in birds. We present two truncated CR1 loci in passerine birds, not only found in representatives of Corvinae (jays, crows and allies), but also in the West-African Picathartes species which provide new evidence for a closer relationship of these species to Corvidae than has previously been thought. Additionally, we show that not only the absence/presence pattern of a CR1 insertion, but also the CR1 sequences themselves contain phylogenetic information.

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

Getting closer to a pre-vertebrate genome: the non-LTR retrotransposons of Branchiostoma floridae

Non-LTR retrotransposons are common in vertebrate genomes and although present in invertebrates they appear at a much lower frequency. The cephalochordate amphioxus is the closest living relative to vertebrates and has been considered a good model for comparative analyses of genome expansions during vertebrate evolution. With the aim to assess the involvement of transposable elements in these events, we have analysed the non-LTR retrotransposons of Branchiostoma floridae. In silico searches have allowed to reconstruct non-LTR elements of six different clades (CR1, I, L1, L2, NeSL and RTE) and assess their structural features. According to the estimated copy number of these elements they account for less than 1% of the haploid genome, which reminds of the low abundance also encountered in the urochordate Ciona intestinalis. Amphioxus (B. floridae) and Ciona share a pre-vertebrate-like organization for the non-LTR retrotransposons (<150 copies, < 1% of the genome) versus the complexity associated to higher vertebrates (Homo sapiens >1.3·10⁶ copies, > 20% of the genome).

A SINE in the genome of the cephalochordate amphioxus is an Alu element

Transposable elements of about 300 bp, termed "short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer.

APE-type non-LTR retrotransposons: determinants involved in target site recognition

Non-long terminal repeat (Non-LTR) retrotransposons represent a diverse and widely distributed group of transposable elements and an almost ubiquitous component of eukaryotic genomes that has a major impact on evolution. Their copy number can range from a few to several million and they often make up a significant fraction of the genomes. The members of the dominating subtype of non-LTR retrotransposons code for an endonuclease with homology to apurinic/apyrimidinic endonucleases (APE), and are thus termed APE-type non-LTR retrotransposons. In the last decade both the number of identified non-LTR retrotransposons and our knowledge of biology and evolution of APE-type non-LTR retrotransposons has increased tremendously.

A recent chicken repeat 1 retrotransposition confirms the Coscoroba-Cape Barren goose clade

Chicken repeat 1 (CR1) is a member of the non-long terminal repeat class of retrotransposons. We have isolated a truncated CR1 element within the third intron of the lactate dehydrogenase B gene of the coscoroba and the Cape Barren goose (Anseriformes; Coscoroba coscoroba, Cereopsis novaehollandiae). Because the element was absent in orthologous loci within mallard (Anas platyrhynchos), snow goose (Anser caerulescens), and tundra swan (Cygnus columbianus), it provides strong support to the recent novel proposal by Donne-Goussé et al. [Donne-Goussé, C., Laudet, V., Hänni, C., 2002. A molecular phylogeny of anseriformes based on mitochondrial DNA analysis. Mol. Phylogenet. Evol. 23, 339-356] that Cape Barren goose is the sister taxon to coscoroba. The time of insertion was approximately 10.5 Mya or less estimated from mitochondrial DNA sequence information. Because this is a recent event, the DNA sequence of this CR1 should be close to that existing at the time of its insertion. This is reflected by the consistency of several structural features expected in a new CR1 copy such as the unaltered flanking target site duplication and inverted repeats that lie 22 bp apart near the 3' end of the element. Hybridization experiments show that numerous copies of sequences closely related to the coscoroba CR1 element are dispersed throughout the genomes of tested Anseriformes, but none were detected in representatives of Galliformes and Struthioniformes.

A new pair of CR1-like LINE and tRNA-derived SINE elements in Podarcis sicula genome

We have identified and characterized a new pair of LINE and SINE elements, called Lucy-1 CR1-like LINE and P.s.1/SINE, respectively, in Podarcis sicula genome. The 3'-tail region in the 3' untranslated region (UTR) of Lucy-1 element is almost identical to the of P.s.1/SINE element. This identity suggests that the P.s.1/SINE element, during evolution, has gained the 3'-end sequence of the Lucy-1 element and has exclusively recruited the enzymatic machinery of its partner CR1 LINE for retroposition. Moreover, the complex molecular organization around Lucy-1 insertion site is discussed and we found that Lucy-1 insertion is associated with the calcium binding transporter gene. Our results confirm that the retrotransposons can be an additional source of genomic diversification and the evolution of the retrotransposable elements can be a vector force shaping genomes by reassorting DNA domains thus forming a new DNA arrangement.

Isolation and characterization of the first non-autonomous transposable element in amphioxus, ATE-1

We report the first class II transposon in cephalochordates, which we have named Amphioxus Transposable Element 1 (ATE-1). ATE-1 members have been identified in the genome of Branchiostoma lanceolatum (BlATE-1) and B. floridae (BfATE-1). Structural analysis revealed that ATE-1 elements consist of a central region (CR) with no homology with any coding sequence, nor any detectable open reading frame (ORF), flanked by internal direct repeats (DR) of about 100 nt, each adjacent to a terminal inverted repeat (TIR) of 16 nt. Although the estimated copy number in the amphioxus genome is low, there is evidence of mobility. Sequence and hybridization analyses pointed to TIR and DR inter-species conservation, whereas no structural similarities among the CR were detected. Moreover, this element is found in two amphioxus species that diverged long ago, which argues in favor of its ancient origin. However, the structural hallmarks needed for transposition are still preserved.

The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes

In silico and experimental approaches have been used to identify the non-long terminal repeat retrotransposons of the urochordate Ciona intestinalis providing valuable data for understanding the evolution of early chordate genomes.

Background

Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes.

Results

Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families.

Conclusions

The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.