PMID- 17996080
OWN - NLM
STAT- MEDLINE
DCOM- 20080206
LR  - 20211020
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 8
DP  - 2007 Nov 9
TI  - Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago 
      truncatula.
PG  - 409
AB  - BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
FAU - Grzebelus, Dariusz
AU  - Grzebelus D
AD  - Department of Genetics, Plant Breeding and Seed Science, Agricultural University 
      of Krakow, Al, 29 Listopada 54, 31-425 Krakow, Poland. dgrzebel@ogr.ar.krakow.pl
FAU - Lasota, Slawomir
AU  - Lasota S
FAU - Gambin, Tomasz
AU  - Gambin T
FAU - Kucherov, Gregory
AU  - Kucherov G
FAU - Gambin, Anna
AU  - Gambin A
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20071109
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (DNA Transposable Elements)
RN  - EC 2.7.7.- (Transposases)
SB  - IM
MH  - Chromosome Inversion
MH  - DNA Transposable Elements/*genetics
MH  - Evolution, Molecular
MH  - Expressed Sequence Tags
MH  - *Genetic Variation
MH  - Genome, Plant/*genetics
MH  - Medicago truncatula/enzymology/*genetics
MH  - Minisatellite Repeats
MH  - Multigene Family
MH  - Mutagenesis, Insertional/genetics
MH  - Open Reading Frames/genetics
MH  - Phylogeny
MH  - Polymorphism, Genetic
MH  - Sequence Alignment
MH  - Terminal Repeat Sequences/genetics
MH  - Transposases/genetics
PMC - PMC2213677
EDAT- 2007/11/13 09:00
MHDA- 2008/02/07 09:00
PMCR- 2007/11/09
CRDT- 2007/11/13 09:00
PHST- 2007/06/11 00:00 [received]
PHST- 2007/11/09 00:00 [accepted]
PHST- 2007/11/13 09:00 [pubmed]
PHST- 2008/02/07 09:00 [medline]
PHST- 2007/11/13 09:00 [entrez]
PHST- 2007/11/09 00:00 [pmc-release]
AID - 1471-2164-8-409 [pii]
AID - 10.1186/1471-2164-8-409 [doi]
PST - epublish
SO  - BMC Genomics. 2007 Nov 9;8:409. doi: 10.1186/1471-2164-8-409.