ArticleBMC genomics2007
Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 30 citations in OpenAlex.
- Evolutionary Study of Transposable Elements: Structural Characterization and Phylogenomic Profiling in Plant Genomes.Journal of molecular evolution · 2026Review
- Review
- Recurrent co-domestication of PIF/Harbinger transposable element proteins in insects.Mobile DNA · 2022Article
- Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry.G3 (Bethesda, Md.) · 2022Article
- The Harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice.Plant biotechnology journal · 2022Article
- Diversity ofAnimals : an open access journal from MDPI · 2022Article
- PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids.BMC genomics · 2019Article
- Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae.BMC evolutionary biology · 2017Article
- The Role of Vertical and Horizontal Transfer in the Evolutionary Dynamics of PIF-Like Transposable Elements in Triticeae.PloS one · 2015Article
- A Deluge of Complex Repeats: The Solanum Genome.PloS one · 2015Article
- Transcriptomic dissection of the rice-Burkholderia glumae interaction.BMC genomics · 2014Article
- hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes.Genetica · 2010Article
- Diversity of DcMaster-like elements of the PIF/Harbinger superfamily in the carrot genome.Genetica · 2009Article
- Article
- LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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