Research article
Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula
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* Corresponding author: Dariusz Grzebelus dgrzebel@ogr.ar.krakow.pl
1 Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
2 Institute of Informatics, Warsaw University, Banacha 2, 02-097, Poland
3 Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
4 LIFL/CNRS/INRIA, Bat. M3 59655 Villeneuve d'Ascq, Lille, France
BMC Genomics 2007, 8:409 doi:10.1186/1471-2164-8-409
Published: 9 November 2007Additional files
Additional file 1:
List of all PIF/Harbinger-like elements identified in the course of the study in the genome of Medicago truncatula.
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Additional file 2:
Similarity-based grouping of M. truncatula PIF/Harbinger-like elements.. Results of multidimensional scaling (MDS): A. whole TE sequence, B. 5'end subterminal regions, C. 3'end subterminal regions, and hierarchical clustering (HC): D. whole TE sequence, E. 5'end subterminal regions, F. 3'end subterminal regions.
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Additional file 3:
Sequence alignment of the A and B blocks differentiating individual elements belonging to the MtPH-M-3 family.
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Additional file 4:
Identification of M. truncatula ESTs similar to putative expression products of orf1 and TPases coded by MtPH elements. Sequence of the whole element was used as query against M. truncatula EST database, hits in orf1 and TPase coding regions with E value lower than 1e-06 were scored. Nearly identical hits to orf1 and TPase of the MtPH-M-1 elements are marked red.
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Additional file 5:
Alignment of MtPH-M-1-Ia and the ESTs corresponding to orf1 (CX532696) and TPase (AW686181). Predicted exons of the orf1 and TPase are highlighted yellow and green, respectively, TSDs of the element are marked gray.
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