Abstract
BackgroundTransposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous PIF/Harbinger-like elements. Based on the above features, PIF/Harbinger-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster.ResultsTwenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous PIF/Harbinger-like elements were found in the genome of M. truncatula. They were divided into five families, MtPH-A5, MtPH-A6, MtPH-D,MtPH-E, and MtPH-M, corresponding to three previously identified and two new lineages. The largest families, MtPH-A6 and MtPH-M were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily MtPH-A6-4. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition.ConclusionThe population of PIF/Harbinger-like elements in the genome of M. truncatula is diverse. A detailed intra-family comparison of the elements' structure proved that they proliferated in the genome generally following the model of abortive gap repair. However, the presence of tandem repeats facilitated more pronounced rearrangements of the element internal regions. The insertion polymorphism of the MtPH elements and related MITE families in different populations of M. truncatula, if further confirmed experimentally, could be used as a source of molecular markers complementary to other marker systems.
Highlights
Transposable elements constitute a significant fraction of plant genomes
Identification and phylogeny of PIF/Harbinger-like elements of M. truncatula The initial search of the M. truncatula genome aimed at the identification of putative autonomous elements, i.e. those carrying an ORF showing homology to the predicted MtMaster TPase protein sequence [14] and flanked with terminal inverted repeats of at least 14 bp, containing the G(N)5GTT motif, and followed by a 3 bplong target site duplications (TSD) (TAA or TTA)
Starting from a single previously described PIF/Harbingerlike Transposable elements (TEs) of M. truncatula, we identified 89 elements representing the diversity of this superfamily in the host plant genome
Summary
Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster. In this paper we used the accumulated M. truncatula genomic sequence data to identify putative TEs belonging to the PIF/Harbinger superfamily and related to a previously characterized MtMaster element [14]. Our study was focused on identification and in-depth characterization of a strictly defined group of full-length (putative autonomous and non-autonomous) TEs carrying a PIF/Harbinger-specific transposase, and a particular TIR motif characteristic of most of the PIF-like, but not of the Pong-like elements. Advances in genome sequencing of model plant species enabled systematic, computer-based studies towards the identification of repetitive sequences, including those representing putative TEs. The presence of certain structural characteristics of particular groups of TEs allowed the development of a range of strategies for de novo or homology-based identification of novel elements. A number of methods for automatic mining of transposable elements were developed [3,4,5,6], To date, two model plant genomes, i.e. A. thaliana and Oryza sativa (rice) have been extensively studied [7,8,9,10,11]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
