Identification and evolutionary analysis of a Triticeae tribe specific novel non-autonomous DNA transposon in DREB related Dehydration Responsive Factor1 gene

Abstract

AbstractA non-autonomous DNA transposon was identified in the DRF1 gene, belonging to the DREB gene family, the presence of this element was initially assessed in the Triticum durum DRF1 gene and subsequently it was also identified in Aegilops speltoides and Triticum urartu DRF1 genes. The DRF1 gene consists of four exons and three introns, the transposon carrying core element is inserted between the first and the third introns. Our studies identified inverted repeats, target site duplications and the presence of many internal reverse and direct short tandem and long tandem repeats, that all represent signals of a transposable element. Based on transposon specific sequence and position of the terminal inverted repeats, a possible transposition mechanism was inferred. As the identified transposable element does not possess a sequence coding for a transposase enzyme, it represents a non-autonomous element. The transposon encompasses a core element with two small, transcribed regions (Exon 2 and Exon 3) that are combined by alternative splicing during gene expression and an intron (intron2). A possible role of this non-autonomous DNA transposon in the alternative splicing regulation was investigated by a genomics approach. Divergence time analysis supported the relatively recent evolution of this transposon in Triticeae comparing to other tribes and further there is no footprints or highly disrupted footprints sequence such as TIR, TSD in other earlier evolved Poaceae member species were observed, which revealed the novelty and well-preserved nature of these signals in Triticeae. While other monocots (apart from Poaceae) and dicots, including Arabidopsis thaliana, neither showed this transposon insertion and nor revealed the existence of alternative spliced gene transcripts. In Poaceae members the core element is well preserved with disturbed transposon and transposon signals, while the tribe Triticeae especially wheat, its progenitors have intact DRF1 transposon and its signals.