28S junctions and chimeric elements of the rDNA targeting non-LTR retrotransposon R2 in crustacean living fossils (Branchiopoda, Notostraca)

Abstract

The 28S rRNA genes of several metazoans are interrupted by site-specific targeting non-LTR retrotransposons, such as R2. R2 elements have been deeply analyzed but aspects of their retrotransposition mechanism and the origin of the wide diversity observed are still debated. We characterized six new R2 lineages in four tadpole shrimp species (Notostraca), samples deriving from a parthenogenetic population of Triops cancriformis (R2Tc_it) and from bisexual Lepidurus populations of L. lubbocki (R2Ll), L. couesii (R2LcA, R2LcB, R2LcC) and L. arcticus (R2La). All elements fit the canonical R2 structure but R2Ll which turned out to be a chimera with an additional ORF originating from another R2. Consistently with data on LINEs, R2Ll could be the result of recombination due to reverse transcriptase template jump. The analysis of 28S/R2 5' end junctions further suggests aberrant homologous recombination, as observed in RNA viruses.

Non-LTR R2 Element Evolutionary Patterns: Phylogenetic Incongruences, Rapid Radiation and the Maintenance of Multiple Lineages

“…clade [18], ii ) the European Notostraca clade (genera Triops and Lepidurus ) [21], iii ) the hard ticks clade [20] and iv ) the Reticulitermes termites clade [19].…”

“…Being ruled out the possibility of R2 elements’ horizontal transfer, the observed phylogenetic pattern has been explained with a high diversification/extinction rate of paralogous lineages, together with instances of strictly vertical inheritance [5], [16], [18], [19], [20], [21]. Incomplete lineage sorting due to fast host speciation may have further hindered the correct phylogenetic signal: therefore, the possible overlapping between metazoan and R2 radiations may contribute to explain the lack of congruence between the two phylogenies.…”

“…Presently identified R2s were then gathered in a single dataset with all elements available from literature (Eickbush lab, http://blogs.rochester.edu/EickbushLab/?page_id=602; [5], [13], [19], [20], [21]; Table S1). R8 and R9 elements, closely related to R2 [1], [2], have been also included in phylogenetic analyses.…”

“…Only in few instances a pattern of strict vertical inheritance occurs: it happens for the insect genera Drosophila and Reticulitermes , the Ixodida ticks and the crustacean genus Lepidurus [18], [19], [20], [21]. As a general remark, though, it is to be pointed out that, even if the main topology can be recognized, trees are weakly supported in most instances [1], [2], [13], [16], [20], [21].…”

“…To further complicate the scenario, some species, such as Lepidurus couesii, Tenebrio molitor, Popilia japonica, Nasonia vitripennis, Ciona intestinalis and Mauremys reevesii , host multiple R2 lineages [17], [21], [22], [23].…”