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Plant centromeric retrotransposons: a structural and cytogenetic perspective

Pavel Neumann1*, Alice Navrátilová1, Andrea Koblížková1, Eduard Kejnovský2, Eva Hřibová3, Roman Hobza2, Alex Widmer4, Jaroslav Doležel3 and Jiří Macas1

Author Affiliations

1 Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice CZ-37005, Czech Republic

2 Institute of Biophysics of the Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ-61265, Czech Republic

3 Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany of the Academy of Sciences of the Czech Republic, Sokolovská 6, Olomouc CZ-77200, Czech Republic

4 ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, CH-8092 Zürich, Switzerland

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Mobile DNA 2011, 2:4  doi:10.1186/1759-8753-2-4

Published: 3 March 2011

Additional files

Additional file 1:

Origin and structural features of sequences used in this work. (A) Origin and (B) sequence and structural features of CRM clade chromoviruses. (C) Elements belonging to the Tekay, Reina and Galadriel clades.

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Additional file 2:

CRM sequences used in this study.

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Additional file 3:

Alignment of reverse transcriptase domains.

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Additional file 4:

Dot plot comparison of full-length CRM elements. The elements are ordered according to group and plant family. Each family is represented by one element.

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Additional file 5:

Transcription of centromeric retrotransposons. (A) Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis using primer pairs amplifying the RT coding domain (see Additional file 6, PCR primer sequences and targets). The three templates shown are reverse-transcribed RNA (+), nontreated RNA (-) and genomic DNA (g). (B) Size distribution of centromeric retrotransposon-derived small RNA. (C) The abundance of centromeric retrotransposon-derived small RNA in various tissues and in Arabidopsis thaliana RNA interference mutants. Data recovered from two different Gene Expression Omnibus accessions (http://www.ncbi.nlm.nih.gov/geo/ webcite) are indicated by black or gray columns. Columns containing data obtained from RNAi mutants are indicated by hatched bars, and the identity of the defective genes is indicated. The small RNA abundance was normalized against the total number of small RNA. TPQ, number of occurrences per quarter million.

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Additional file 6:

Polymerase chain reaction primer sequences and targets.

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