Diverse DNA transposons in rotifers of the class Bdelloidea

Abstract

We surveyed the diversity, structural organization, and patterns of evolution of DNA transposons in rotifers of the class Bdelloidea, a group of basal triploblast animals that appears to have evolved for millions of years without sexual reproduction. Representatives of five superfamilies were identified: ITm (IS630/Tc/mariner), hAT, piggyBac, helitron, and foldback. Except for mariners, no fully intact copies were found. Mariners, both intact and decayed, are present in high copy number, and those described here may be grouped in several closely related lineages. Comparisons across lineages show strong evidence of purifying selection, whereas there is little or no evidence of such selection within lineages. This pattern could have resulted from repeated horizontal transfers from an exogenous source, followed by limited intragenomic proliferation, or, less plausibly, from within-host formation of new lineages under host- or element-based selection for function, in either case followed by eventual inactivation and decay. Unexpectedly, the flanking sequences surrounding the majority of mariners are very similar, indicating either insertion specificity or proliferation as part of larger DNA segments. Members of all superfamilies are present near chromosome ends, associated with the apparently domesticated retroelement Athena, in large clusters composed of diverse DNA transposons, often inserted into each other, whereas the examined gene-rich regions are nearly transposon-free.

Fig. 1.

Structure and coding capacity of bdelloid DNA TEs. (A) IS630/Tc/mariner. (B) Helitron, hAT, foldback, and piggyBac superfamilies. TIRs are designated by filled triangles; frameshifts are designated by vertical lines; in-frame stop codons are designated by asterisks; introns are designated by open triangles; NLS are designated by diamonds; poly(A) signals are designated by colons; and helix-turn-helix motifs are designated by checkered boxes. Letters indicate the corresponding conserved amino acids and TSDs. For Avmar1, thin horizontal lines with arrows indicate PCR amplification strategy, and thick lines mark the position of internal deletions in two amplified copies.

Fig. 2.

Terminal sequences of bdelloid DNA transposons. (A) Sequences of Avmar1 TIRs from different 5′ and 3′ UFW clones, showing divergence in a sequence logo format (http://weblogo.berkeley.edu/logo.cgi). Positions differing between 5′ and 3′ TIRs are marked by asterisks. (B–E) TIRs of ITm (mariner, DD37D, DD37E), foldback, piggyBac, and hAT superfamily members from bdelloids (underlined) and other species, including C. elegans, D. melanogaster, Haematobia irritans, Homo sapiens, Anopheles albimanus, Aedes triseratus, C. briggsae, Bombyx mori, Chironomus thummi, Xenopus laevis, and Daphnia pulex (, –20) in the BoxShade format. Numbers indicate TIR length. (F) Conserved 3′ termini of Helitrons from P. roseola, A. vaga, C. elegans, Oryza sativa, and A. thaliana, with underlined hairpins (21).

Fig. 3.

Phylogeny and selection patterns in Avmar1. Neighbor-joining (NJ) trees of full-length Avmar1 copies (A) and 900-bp N-terminal (B) and 300-bp C-terminal (C) UFW fragments, excluding TIRs, are shown. Copies with intact ORFs are underlined; * and # denote in-frame stop codons and frameshifts, respectively. Lineages are designated a–d; three copies in A (IR23, IR34, and IR39) cannot be assigned to a specific lineage because of recombination (see text); two additional divergent lineages in B and C obtained by UFW but not by TIR-PCR are designated e and e′. For lineage assignment, appropriate segments of several IR copies from A are included in B and C phylogenies. Bootstrap support values >50% from 10,000 replications are indicated; Bayesian analysis gave the same tree topology (data not shown) and the clade credibility values for clades that had >50% support in NJ trees were all higher. Tall arrowheads in B and C denote copies sharing common flanking sequences. (D) Plot of Ka against Ks in all pairwise combinations within and between the Avmar1 lineages a–d.