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. 2014 Jun 3:5:17.
doi: 10.1186/1759-8753-5-17. eCollection 2014.

Tc1-like transposable elements in plant genomes

Yuan Liu  1 , Guojun Yang  1
Affiliations

Tc1-like transposable elements in plant genomes

Yuan Liu et al. Mob DNA. .

Abstract

Background: The Tc1/mariner superfamily of transposable elements (TEs) is widespread in animal genomes. Mariner-like elements, which bear a DDD triad catalytic motif, have been identified in a wide range of flowering plant species. However, as the founding member of the superfamily, Tc1-like elements that bear a DD34E triad catalytic motif are only known to unikonts (animals, fungi, and Entamoeba).

Results: Here we report the identification of Tc1-like elements (TLEs) in plant genomes. These elements bear the four terminal nucleotides and the characteristic DD34E triad motif of Tc1 element. The two TLE families (PpTc1, PpTc2) identified in the moss (Physcomitrella patens) genome contain highly similar copies. Multiple copies of PpTc1 are actively transcribed and the transcripts encode intact full length transposase coding sequences. TLEs are also found in angiosperm genome sequence databases of rice (Oryza sativa), dwarf birch (Betula nana), cabbage (Brassica rapa), hemp (Cannabis sativa), barley (Hordium valgare), lettuce (Lactuta sativa), poplar (Populus trichocarpa), pear (Pyrus x bretschneideri), and wheat (Triticum urartu).

Conclusions: This study extends the occurrence of TLEs to the plant phylum. The elements in the moss genome have amplified recently and may still be capable of transposition. The TLEs are also present in angiosperm genomes, but apparently much less abundant than in moss.

Keywords: Evolution; Mariner-like elements; Moss; Plant genome; Tc1-like elements; Tc1-mariner-IS630 superfamily; Transposable elements; Transposition activity.

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Figures

Figure 1
Figure 1
Tc1-like elements in the moss genome. Schematics of PpTc1 and PpTc2 element structures. Black triangles, TIRs; regions in green or red, non-coding sequences; regions in yellow or brown, open reading frames; HTH, helix-turn-helix DNA binding motif; DDE, catalytic DD34E triad motif.
Figure 2
Figure 2
Sequence divergence of full-length elements of PpTc 1 and PpTc 2. Y-axis, number of elements; x-axis, level of sequence divergence from the consensus sequence of PpTc1 or PpTc2 family.
Figure 3
Figure 3
Comparison of the putative transposases of PpTc 1 and PpTc 2. (A) Alignment of peptide sequences. Colored residues: blue to cyan, α-helices of HTH motifs; green to yellow, DD34E triad motif. (B) Predicted three-dimensional ribbon models of transposases. Blue to red, N terminus to C terminus; HTH1 and HTH2, putative DNA binding (both) and dimerization (HTH1 only); clamp, loop structure potentially interacts with the linker of the other monomer in a transposase dimer; linker, potentially interacts with the clamp loop of the other monomer in a dimer; DD34E, catalytic active center.
Figure 4
Figure 4
Transcripts from PpTc elements. Thick lines on top, query sequences; solid thin lines, matched regions between the queries and hits in the transcript database; dotted lines, unmatched regions reflecting intronic regions; the coding DNA sequence (CDS) of moss actin1 gene was used as a control.
Figure 5
Figure 5
Phylogenetic relationship of transpoases of moss TLEs to those of animal and fungal TLEs. Names, species followed by GI numbers of each sequence; numbers on branches, percentage of bootstrap value of 1,000 reiterations.
Figure 6
Figure 6
Sequence alignment of the catalytic motifs of transposases (A) and end sequences (B) of plant TLEs. (A) The regions containing the DDE/D catalytic motifs of the transposase sequences. Plant MLEs are shown at the bottom. (B) The terminal sequences of plant TLEs and Tc1. The degree of background shading indicates different levels of conservation of sequences. Asterisks indicate elements that only have one end present in a genomic contig. Abbreviation for species names: Os, Oryza sativa; Bn, Betula nana; Br, Brassica rapa); Cs, Cannabis sativa; Hv, Hordium valgare; Ls, Lactuta sativa; Pt, Populus trichocarpa; Pb, Pyrus x bretschneideri; Tu, Triticum urartu.
Figure 7
Figure 7
Patchy distribution of plant species containing TLEs. Based on the cladogram of sequenced plant genomes (up to April 2013) generated by James Schnable at CoGe (http://genomevolution.org) and used with permission. Black, published genomes; Gray, unfinished genomes; Green highlight, species containing TLEs.
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