Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

Grzebelus, Dariusz; Lasota, Sławomir; Gambin, Tomasz; Kucherov, Grégory; Gambin, Anna

doi:10.1186/1471-2164-8-409

Cited by 27 publications

(42 citation statements)

References 41 publications

(48 reference statements)

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“…We thus decided to analyze the conservation of other M. truncatula transposons with respect to their Arabidopsis counterparts. We have not found any Arabidopsis sequence having a significant similarity at the nucleotide level to the recently described M. truncatula PIF elements (Grzebelus et al 2007) or any M. truncatula sequence having significant similarity to the mudrA-like coding sequence of the Arabidopsis MuDR element (At2g11560). However, we have found M. truncatula sequences having significant similarity to the sequences of the Arabidopsis CACTA elements CACTA1 (AB052792) and CAC5 (AB095515) (not shown), although the level of similarity (65% identity in 471 bp and 66% identity in 533 bp, respectively) is well below of that of the Lemi1-related sequences.…”

Section: Methodscontrasting

confidence: 53%

“…However, although a handful of M. truncatula transposons have been described (Charrier et al 1999;Jurka 2000;Holligan et al 2006;Vitte and Bennetzen 2006;Grzebelus et al 2007;Macas and Neumann 2007) to date, most of them have not been fully characterized. Here we present a global analysis of a pogo-like family of transposons, closely related to the AtLemi1 element that we have named as MtLemi1.…”

Section: Discussionmentioning

confidence: 99%

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Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

Guermonprez

Loot²,

Casacuberta

2008

Genetics

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Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II elements present in genomes as high-copy-number populations of small and highly homogeneous elements. While virtually all class II transposon families contain non-autonomous defective transposon copies, only a subset of them have a related MITE family. At present it is not known in which circumstances MITEs are generated instead of typical class II defective transposons. The ability to produce MITEs could be an exclusive characteristic of particular transposases, could be related to a particular structure of certain defective class II elements, or could be the consequence of particular constraints imposed by certain host genomes on transposon populations. We describe here a new family of pogo-like transposons from Medicago truncatula closely related to the Arabidopsis Lemi1 element that we have named MtLemi1. In contrast to the Arabidopsis Lemi1, present as a single-copy element and associated with hundreds of related Emigrant MITEs, MtLemi1 has attained .30 copies and has not generated MITEs. This shows that a particular transposon can adopt completely different strategies to colonize genomes. The comparison of AtLemi1 and MtLemi1 reveals transposase-specific domains and possible regulatory sequences that could be linked to the ability to produce MITEs.

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Section: Methodscontrasting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

Guermonprez

Loot²,

Casacuberta

2008

Genetics

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“…The PIF/Harbinger elements are flanked by short terminal inverted repeats (TIRs) and a 3 bp long target site duplication (TSD), usually TAA or TTA (Zhang et al 2004). They were shown to be related to miniature inverted repeat transposable elements (MITEs) of the Tourist family of maize (Bureau and Wessler 1992;Zhang et al 2001;Jurka and Kapitonov 2001) and few families of M. truncatula (Grzebelus et al 2007b). PIF/Harbinger elements were grouped into several lineages, based on the transposase homology and the order of open reading frames (Zhang et al 2004;Grzebelus et al 2007b).…”

Section: Introductionmentioning

confidence: 98%

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

Grzebelus

Simon

2008

Genetica

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Transposable elements constitute a significant fraction of plant genomes. Both autonomous and non-autonomous elements of the DcMaster family, residing in the carrot genome, were described previously. DcMaster elements were classified as members of the PIF/Harbinger superfamily. In the present paper we report on the identification of other groups of DcMaster-like elements. Beside the previously described, relatively highly abundant miniature inverted repeat element (MITE) family Krak (ca. 3,600 copies, ca. 80% intra-family similarity), three other families, i.e. 1.1 kb long KrakL1 (ca. 3,000 copies, ca. 98% intra-family similarity), 1.2 kb long KrakL2 (a single identified element, 71.1% similar to KrakL1 consensus), and 2.2 kb long Midi (few elements, 99% intra-family similarity), were revealed. The fact that all members within each of the newly found families were almost identical in their sequence suggests their very recent activity. The families differed in terms of their similarity to the canonical DcMaster element. They also differed in copy number, from just a few copies of Midi to few thousand copies of Krak. A modification of the DcMaster Transposon Display (DcMTD) marker system, targeted specifically towards Krak elements, was used to investigate their insertion polymorphism. It was shown that Krak insertion sites, similarly to those of the DcMaster elements, were highly polymorphic between the wild and the cultivated Daucus carota.

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“…Some studies have focused on the characterization of families of transposons and their derivatives in particular genomes (Quesneville et al 2006;Grzebelus et al 2007;Yang and Barbash 2008). These studies are important to understand the role of the relationship between autonomous elements and their derivatives in genomic evolution.…”

Section: Introductionmentioning

confidence: 98%

hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes

et al. 2010

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Transposable elements (TEs) comprise a significant fraction of the genome, and some models of the TE "life cycle" suggest that, in the last phases of the cycle, TEs should be represented, in the genomes, by inactive and degenerated copies. In this study, we analyzed, using a bioinformatics approach, the autonomous hAT elements and their derivatives (active non-autonomous, MITE relatives and degenerated copies) in 12 Drosophila genomes. We found 28 hAT elements that had derivatives. Most copies had features that suggested that they were active, while only a few degenerated copies were found. Because hAT elements comprise an evolutionarily old superfamily, one should expect to find many degenerated copies within the genome, although this was not observed in our study. These results suggest that primarily active copies of hAT elements are maintained in the euchromatic regions of the genome and that degenerated copies are removed from the genome by natural selection.

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Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

Cited by 27 publications

References 41 publications

Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome

hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes

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