- Research article
- Open Access
Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula
© Grzebelus et al; licensee BioMed Central Ltd. 2007
- Received: 11 June 2007
- Accepted: 09 November 2007
- Published: 09 November 2007
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. 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.
Twenty 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.
The 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.
- Transposable Element
- Terminal Inverted Repeat
- Target Site Duplication
- Autonomous Element
- Mite Family
Transposable elements (TEs) are dispersed repetitive sequences constituting a major fraction of plant genomes, ranging from 10% of Arabidopsis thaliana genome , to an estimated value over 70% of maize genome . Class I elements (retrotransposons), transposing via an RNA intermediate, form the most abundant fraction, while class II elements (DNA transposons), use a 'cut and paste' mechanism for transposition and are usually less numerous.
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 [3–6], To date, two model plant genomes, i.e. A. thaliana and Oryza sativa (rice) have been extensively studied [7–11].
Founder members of the PIF/Harbinger superfamily of class II TEs were identified in maize  and A. thaliana . Other full-length elements were subsequently found in rice (Pong ), carrot, and M. truncatula (Master ). Autonomous PIF/Harbinger-like elements carry 14–25 bp long terminal inverted repeats (TIRs) flanked by 3 bp long (TTA/TAA) target site duplications (TSD), and a DDD/DDE transposase showing similarity to that of the bacterial IS5 insertion sequence. The group of PIF/Harbinger-like elements was shown to be widespread in the plant kingdom and composed of two easily distinguishable subgroups, i.e. PIF and Pong . Elements representing both subgroups were related to certain miniature inverted repeat elements (MITEs), like Tourist in maize [12, 16] and mPING in rice .
Medicago truncatula (barrel medic) has been chosen as a model plant for the Fabaceae family, primarily to study relationships between plants and their symbiotic microbes. It has a relatively small genome of 500 to 600 Mbp , shows annual growth habit and self-fertility. The genome of M. truncatula has not been extensively analysed with respect to TE identification. A MITE element Bigfoot was reported in the genomes of M. truncatula and M. sativa , a set of Ty3/gypsy-like Ogre elements characteristic for legume species was described in M. truncatula , and several other M. truncatula elements were briefly characterized in Repbase Update database . A recent study of another model legume, Lotus japonicus, identified a number of PIF- and Pong-like elements and a strong evidence for their recent amplification in the host genome .
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 . Therefore, 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 not only a PIF/Harbinger-specific transposase, but also a particular TIR motif characteristic of most of the PIF-like, but not of the Pong-like elements.
Identification and phylogeny of PIF/Harbinger-like elements of M. truncatula
Characteristics of the core PIF/Harbinger-like elements of M. truncatula
GenBank sequence no.
Position (first base-last base)
No. of introns in TPase
TP > orf1
TP > orf1
TP > orf1
TP > orf1
TP > orf1
TP > orf1
orf1 > TP
orf1 > TP
orf1 > TP
orf1 > TP
orf1 > TP
Diversity and abundance of PIF/Harbinger-like elements in M. truncatula
Classification and abundance of M. truncatula PIF/Harbinger-like elements
Number of elements
Containing Tpase and orf1
With no coding capacity
Consensus TIR sequences of M. truncatula PIF/Harbinger-like elements
5' GGGKGYGTTTGTTTGAGGGTT 3'
5' GGGTCCGTTTGGTTC 3'
5' GGCTMTGTTTGGATT 3'
5' GGGTCCGTTTGGTTCGAGARTT 3'
5' GGCTTTGTTTGCGAGTT 3'
5' GGCTWTGTTTGG 3'
5' GGGCCTGTTTGRAACACTTTTT 3'
5' GTGYRTGTTTGGYA 3'
5' GYRYGTGTTTGGTT 3'
5' GNSYSTGTTTGGTT 3'
The largest family, MtPH-A6, contained 54 elements, while family MtPH-D was represented only by a single element. The second most abundant family, containing 27 elements, was MtPH-M (Master), of which 18 was grouped into subfamily 3.
Detailed structure analysis of MtPH families
MtPH-A6 consisted of four subfamilies represented by putative autonomous elements sharing similar ORF organization, i.e. a TPase containing two introns, followed by orf1. MtPH-A6 TPases formed a well supported clade, containing four subclades with high bootstrap values, representing the corresponding subfamilies (Figure 1).
Subfamily MtPH-A6-1 contained nine elements ranging in length from 802 to 8,707 bp, the longest element carrying a nested insertion of the 7,555 bp long RAM12 gypsy-like retrotransposon.
Subfamily MtPH-A6-2 grouped six elements, 898 to 4,218 bp long, all being simple internal deletion derivatives of the core element MtPH-A6-2-Ia.
MtPH-M family included three subfamilies with short (14 bp), similar TIRs and orf1 followed by TPase. Subfamily MtPH-M-1 contained only four elements, ranging in length from 812 to 5,140 bp. Two of them, MtPH-M-1-Ia (previously described as MtMaster ) and MtPH-M-1-IIa (showing 90% overall sequence identity to MtMaster) had both ORFs, and the remaining two were internally deleted derivatives.
Family MtPH-A5 was represented by four elements ranging in length from 1,182 to 6,770 bp. The two putative autonomous elements were 72% similar over the entire sequence, but within the coding region the nucleotide sequence similarity reached 95%. Two shorter elements were deletion derivatives of full-length elements. Interestingly, a recently reported MITRAV family of miniature elements of barrel medic  showed a high nucleotide sequence similarity of their termini to the MtPH-A5 elements, spanning over ca. 40 bp on both ends of the element.
Family MtPH-E consisted of three elements, none of which carried both ORFs. The elements ranged from 1,508 to 3,957 bp. The two largest elements were very similar, differing by one indel, while the similarity of the shortest element to the other two was restricted only to the 180 bp of the 5' terminus and 70 bp of the 3' terminus.
Family MtPH-D was represented by a single element of 3,160 bp, carrying both ORFs. However, their orientation was opposite to that of typical PIF/Harbinger-like elements representing the D lineage . Its localization in the D lineage was not strongly supported by bootstrap analysis (Figure 1). The fact that no internally truncated elements were identified could suggest that the element might be capable of perfect excision, not triggering the process of abortive gap repair.
Documentation of the mobility of the mined elements
We identified several M. truncatula ESTs showing high similarity to putative expression products (orf1 and TPase) of the mined autonomous elements (Additional File 4). However, ESTs directly corresponding to the putative expression products, both to the orf1 (CX532696, 641 bp, 94% identity) and the TPase (AW686181, 304 bp, 99% identity), could be detected only in case of elements representing the MtPH-M-1 subfamily (Additional File 5). Interestingly, A number of ESTs similar to non-coding terminal regions of the TEs could also be identified (data not presented).
We developed a strategy for identification of transposable element families through in silico genome mining, based on initial assumptions on the type of transposase and the consensus sequences of terminal inverted repeats. It required several consecutive steps, i.e. (1) search for regions coding for the TPase, (2) identification of TIRs flanking the identified regions and matching a defined sequence motif, (3) identification of related elements with no coding capacity, and (4) grouping the identified elements into families on the basis of their sequence similarity. We applied this strategy to mine the genome of Medicago truncatula for PIF/Harbinger-like elements similar to the previously described MtMaster element . In principle, the proposed strategy can be used to mine for any other type of class II TEs, provided that at least one 'seed' element is known.
Diversity of the identified PIF/Harbinger-like elements is high, although our search was limited by a specifically defined core TIR sequence. We focused on 22 ORFs coding for putative TPases, representing a half of all initially identified ORFs, as for the other half, TIRs flanking the ORF and containing the required motif could not be found. A recent broad analysis of the TE landscape in another legume, Lotus japonicus , revealed a presence of nine putative autonomous PIF-like elements (besides several more distantly related Pong-like elements) in ca. 32 Mb portion of the genome. This number is in agrrement with our results, as we found 22 full-length elements (2.5 times more) in ca. 200 Mb representing a certain level of redundancy. Interestingly, all PIF-like TEs from L. japonicus represented the A3 lineage, while no A3 members were identified in M. truncatula, which may indicate a strikingly different evolutionary fate of that group of TEs in each of the closely related species.
Detailed structure analysis of the mined element families indicates that their proliferation in the genome generally follows the model of abortive gap repair (AGR), as proposed for the Ac/Ds elements in maize . Members of a particular family were usually direct deletion derivatives of the related, putative autonomous element. However, assuming that members of all PIF/Harbinger-like TE families in the genome of M. truncatula were mobilized with similar frequency, the efficiency of AGR seems to vary from one family to another. Two families, MtPH-A6 and MtPH-M, were the most numerous, while the remaining three were represented by a very small number of copies. Difference in the copy number may be a result of different transposition rates, but it may also indicate that some elements less efficiently trigger the process of AGR following excision, which would result in a higher frequency of perfect excision. The latter is further supported by two observations. Firstly, the members of subfamily MtPH-A6-4 contain a variable number of 60 bp tandem repeats in one or both subterminal regions, serving as targets for AGR and leading to increase of the TE copy number accompanied by changes in the number of VNTRs. The presence of 60 bp tandem repeats was inherently connected with MtPH-A6-4 elements throughout the M. truncatula genome, which implies that they likely evolved in the course of the proliferation of that subfamily. Probably, triggering the AGR from the VNTR region also led to an inversion of the internal region in MtPH-A6-4-XIV, as compared to MtPH-A6-4-Ia. Secondly, at least one member of the low copy number family MtPH-E was transpositionally active, as confirmed by the presence of the RESite, but despite the potential for mobility, the number of MtPH-E elements has remained low.
PIF/Harbinger-like elements are ancestors of certain groups of miniature transposons (MITEs), the relation of maize PIF element and MITEs belonging to the Tourist family has been well documented [12, 16]. Also, several other MITE families, e.g. Heartbreaker from maize , Kiddo from rice , and Krak from carrot  show TIR sequence similarities to those of PIF/Harbinger-like elements. We were able to directly link the previously identified MITRAV MITE family  to family MtPH-A5 of M. truncatula PIF/Harbinger-like elements. This suggests that both MtPH-A5 and MITRAV originated from a recent common ancestor and MtPH-A5 TPase might be the trans-acting factor for MITRAV mobilization, as experimentally proven for the Pong and mPing MITE in rice [13, 26, 27]. Also, two groups of two and ten TEs, all classified in the subfamily MtPH-M-3, might represent newly emerging MITE families. We performed an initial search for other MITEs showing a TIR homology to the consensus motif of the PIF/Harbinger TIRs leading to an identification of few other MITE families (data not presented). Altogether, it confirms that PIF/Harbinger-like elements and related MITEs are present in the genome of M. truncatula, similar to genomes of other plant species. However, the number of MITE copies is probably much lower than that present in the grass genomes.
A more detailed experimental evaluation of MtPH TEs diversity in a range of M. truncatula populations should be useful to further characterize the transpositional activity and the dynamics of particular families. Analysis of RESites and a high incidence of insertion related size polymorphisms shows that a significant fraction of the mined elements was mobile in the recent past. The presence of ESTs related to ORFs of the MtPH elements, including those directly derived from the MtPH-M-1 elements, suggests that they can still be mobile. As proven previously, one transcriptionally active autonomous element can cause trans-mobilization of a range of related, but not directly derived elements .
Polymorphic insertion sites could be used as a source of molecular markers, as shown previously for other species [28–30], to measure intraspecific diversity in relation to its geographic structure, complementing other molecular marker systems, e.g. these based on microsatellites .
Starting from a single previously described PIF/Harbinger-like TE of M. truncatula, we identified 89 elements representing the diversity of this superfamily in the host plant genome. They were divided into five families representing different evolutionary lineages, and further into subfamilies. Elements within each subfamily evolved essentially following the model of AGR, leading to the reconstruction of an internally deleted copy in the donor site following transposition. It is likely that different families vary in their potential to trigger the process of AGR. One peculiarity observed in a group of elements representing subfamily MtPH-A6-4 was the presence of 60 bp long VNTRs in one or both subterminal regions or even spanning over the entire internal region of the TE. Some of the identified elements are closely related to several MITE families, including a previously described MITRAV family. Also, some of the newly identified short elements can be viewed as in statu nascendi MITEs, provided that conditions for a rapid burst of their mobility would be met. Further investigation is necessary for a more detailed evaluation of the copy number, transpositional activity, and insertional polymorphism of the TEs, including MITEs, as they could be utilized as a source of molecular markers.
Semi-automated mining of PIF/Harbinger-like elements
The experiment was performed on the M. truncatula genomic DNA sequence database consisting of 1540 BACs, updated Aug 2005 . As the size of the whole M. truncatula genome ranges from 500 to 600 Mbp  and the average non-overlapping coverage by each BAC was ca. 100 Kb , we estimated that the input sequence data amounted 26–30% of whole genome.
The predicted protein sequence of DDE domain and the whole TPase sequence of the previously identified MtMaster element  was used as the initial query for a TBLASTN search against the BAC sequence database, using the E-value threshold of 1e-20. The output file was then processed to eliminate redundancy coming from overlapping BACs, and significant hits were extracted, along with up to 30 kb flanking sequences. The extracted sequences were scanned for the presence TIRs and TSDs, using a newly developed tool named TIRfinder, identifying TIRs and TSDs and returning a file with a list of found elements fulfilling user-defined requirements. To provide fast computation on whole genome, the algorithm uses very efficient data structures, such as suffix trees. TIRfinder is an open source software accessible online . The program was written in Java and can be run on Windows or Linux.
We allowed up to four mismatches inside 14 bp of the TIRs and no mismatch in TSDs. Another condition was the presence of the conserved G(N)5GTT motif at the 5' end of the TIR. In silico prediction of the presence of coding regions was performed for all identified sequences using FGENESH .
To identify internally deleted copies of elements related to those found previously, 217 bp-long (3 bp TSD + 14 bp TIR + 200 bp subterminal sequence) terminal regions were extracted from all putative autonomous elements. These sequences were used to scan the M. truncatula genomic DNA sequence database (BLASTN, E-value threshold – 1e-10), and regions showing homology to any of the terminal regions were identified. The output was automatically filtered to find sequences of length ranging from 400 to 30,000 bp, flanked with TIRs showing homology to the same autonomous element on both ends. All newly found sequences have been checked whether they contained a region coding for the TPase. All TEs were scanned using Censor , to identify the presence of nested elements.
Phylogenetic analyses, grouping, and visualization of TE sequence similarity
Multiple alignment of 48 transposase sequences of PIF/Harbinger-like transposable elements was obtained using T-Coffee . Bootstrap analysis was performed with PHYLIP using seqboot, neighbor, protdist and consense programs . The sequence similarity of 89 TEs was analyzed by the hierarchical clustering method and visualized with help of multidimensional scaling. For both tasks we used the R statistical environment . As a measure of dissimilarity between sequences we used the E-value of BLAST. Hierarchical cluster analysis of a set of dissimilarities was done by hclust (complete linkage) method . Multidimensional scaling  visualization is primarily dependent on the analogy of similarity and proximity (and hence of dissimilarity and distance). It re-scales a set of dissimilarity data into distances and produces the low-dimensional configuration that generated them. The visualization for our data was obtained with isoMDS R procedure.
TE structure analysis
Sequences were visually compared, aligned, edited, and analysed using BioEdit and the included accessory applications . Pairwise sequence comparisons were performed using 'blast 2 sequences'  and Yass [43, 44]. Dot-plots were generated using Nucleic Acid Dot Plots  with a window size of 25 nucleotides and a mismatch limit of 5 positions. Tandem repeats identification was performed using 'mreps' software [46, 47].
Documentation of mobility
In order to find RESites (Related to Empty Sites) in the M. truncatula genome we performed a computer-based search, essentially as described by Le et al. . Briefly, we extracted 1 Kb sequence flanking both sides of each of the mined elements, combined them into one sequence of 2 Kb, and used it as a query for a BLASTN search on the whole BAC sequence database. Hits spanning on both sides of the insertion were considered as those representing RESites.
EST search was performed using nucleotide sequences of the putative autonomous elements, using a BLAST tool run against the M. truncatula EST database .
PCR assay was performed on plants representing cv. Jemalong A17 and seven populations from the core M. truncatula collection (CC8, as described by Ronfort et al. ). Primer pairs were anchored in the regions flanking the mined elements. They were designed using Primer3  to obtain amplification of ca. 600 bp long fragment for the putative empty site. Two cycling protocols were employed. For TEs of length not exceeding 2 Kb a standard PCR was performed. The reaction was set up in the volume of 20 μl and contained 0.25 mM each dNTP, 2 mM MgCl2, 10 pmol of each primer, 1 unit of TAQ polymerase (Fermentas) and 2 μl of the PCR buffer supplied by the manufacturer. The thermal profile of the reaction was as followed: 94°C for 2 min., 35 cycles of: 94°C for 30 s, 53°C for 30 s, and 68°C for 90 s, and completed with 68°C for 5 min. For larger elements we used long PCR protocol. Amplification was performed in the volume of 20 μl containing 0.25 mM each dNTP, 10 pmol of each primer, 0,5 unit of long PCR enzyme mix (Fermentas) and 2 μl of the Long PCR buffer supplemented with MgCl2 (Fermentas), using the following thermal profile: 94°C for 2 min., 35 cycles of: 94°C for 15 s, 53°C for 30 s, and 68°C for 7 min., and completed with 68°C for 10 min. All reactions were carried out in the Mastercycler or Mastercycler Gradient (Eppendorf). Amplification products were separated on 1% agarose gels and visualized with ethidium bromide under UV.
The research project was funded by the Polish Ministry of Science and Higher Education grant no. N301 036 31/1203, for the years 2006–2008. SL, AG and GK were supported by the Polonium and ECO-NET programs of the French Ministry of Foreign Affairs. The authors wish to thank Dr. J-M Prosperi for donating seeds of M. truncatula populations used in the study, two anonymous reviewers for their helpful suggestions, and Mrs M Gladysz for her technical assistance.
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