Abstract
BackgroundTransposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes. PIF and Pong-like elements belong to two closely-related element families within the PIF/Harbinger superfamily of Class II (DNA) transposons. Both elements contain two open reading frames; one encodes a transposase (ORF2) that catalyzes transposition of the functional elements and their related non-autonomous elements, while the function of the second is still debated. In this work, we surveyed for PIF- and Pong-related transcriptional activity in 13 diploid Triticeae species, all of which have been previously shown to harbor extensive within-genome diversity of both groups of elements.ResultsThe results revealed that PIF elements have considerable transcriptional activity in Triticeae, suggesting that they can escape the initial levels of plant cell control and are regulated at the post-transcriptional level. Phylogenetic analysis of 156 PIF cDNA transposase fragments along with 240 genomic partial transposase sequences showed that most, if not all, PIF clades are transcriptionally competent, and that multiple transposases coexisting within a single genome have the potential to act simultaneously. In contrast, we did not detect any transcriptional activity of Pong elements in any sample.ConclusionsThe lack of Pong element transcription shows that even closely related transposon families can exhibit wide variation in their transposase transcriptional activity within the same genome.
Highlights
Transposable elements are major contributors to genome size and variability, accounting for approximately 70–80% of the maize, barley, and wheat genomes
We have demonstrated that PIF and Pong elements in the genomes of diploid Triticeae species are abundant and highly variable, and represent multiple diverse lineages within genomes that appear to predate the origin of the tribe itself [45, 46]
In contrast to our evidence of PIF transcription, we did not detect any transcriptional activity of Pong elements in any sample
Summary
Isolation and characterization of PIF cDNAs We isolated, cloned, and sequenced 156 unique cDNA fragments from the conserved transposase domain of PIFlike TEs in 15 diploid Triticeae samples. Group I contained sequences from all samples except E. bonaepartis Within this group, P. libanotica 14L was identical to T. caput-medusae1 6L (indicated with rectangles on Fig. 2). The best topology (−lnL = 11,008.92254; Fig. 3) revealed multiple distinct transposase cDNA fragments grouped with genomic sequences in well-defined and generally well-supported clades (Fig. 3). Eight cDNAs were identical to genomic PIF fragments (indicated with green rectangles in Fig. 3), suggesting that they originated from identical or nearly identical transposase fragments ( only half of them are paired with genomic copies from the same species). Of these eight transcripts, seven were derived from transposases with no frameshifting indels or stop codons. Two pairs of genomic transposase sequences were identical (marked with pale blue rectangles on Fig. 3): gThinopyrum bessarabicum 8 and gP.libanotica 14; and gH. bogdanii 15 and gT. urartu 23
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