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Open Access Research article

Identification, characterization and distribution of transposable elements in the flax (Linum usitatissimum L.) genome

Leonardo Galindo González and Michael K Deyholos*

Author Affiliations

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada

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BMC Genomics 2012, 13:644  doi:10.1186/1471-2164-13-644

Published: 21 November 2012

Additional files

Additional file 1:

Annotation of de novo repeats. Annotation of de-novo repeats.

Format: XLSX Size: 11.3MB Download file

Open Data

Additional file 2:

Correlation between TE and gene coverage on scaffolds ≥ 1Mb. Scatter plots of correlation of the proportion of coverage between genes and the four largest transposable elements (TEs) superfamilies in scaffolds larger than 1 million bp.

Format: DOCX Size: 35KB Download file

Open Data

Additional file 3:

Proportional coverage of genes and TEs. Proportional coverage of genes and TEs in scaffolds over 1 Mb.

Format: XLSX Size: 16KB Download file

Open Data

Additional file 4:

Monte Carlo tests. Monte Carlo test for probability that TEs are overlapping genes more than expected by chance.

Format: XLSX Size: 223KB Download file

Open Data

Additional file 5:

Filtered LTR elements. Filtered LTR elements.

Format: XLSX Size: 2.9MB Download file

Open Data

Additional file 6:

Distances of LTR elements to their closest gene. Distances of LTR elements to their closest gene.

Format: XLSX Size: 80KB Download file

Open Data

Additional file 7:

BLAT analysis of recent LTR TE insertions in genome. BLAT analysis of recent LTR TE insertions in genome.

Format: XLSX Size: 371KB Download file

Open Data

Additional file 8:

BLAT analysis of recent LTR TEs against ESTs. BLAT analysis of recent LTR TEs against ESTs.

Format: XLSX Size: 48KB Download file

Open Data

Additional file 9:

Protein domains in LTR elements. Identification of protein domains in LTR elements. The name of the sequences are made using superfamily, algorithm, coordinates and similarity percentage between LTR pairs.

Format: XLSX Size: 290KB Download file

Open Data

Additional file 10:

Percentage of bp covered by LTR retrotransposon superfamilies. Percentage of bp covered by LTR retrotransposon superfamilies in characterized genomes. Plant species are organized according to phylogenetic relationships. The figures for each genome correspond to Brachypodium distachyon [62], Oryza sativa [63], Zea mays [11], Sorghum bicolor [64], Vitis vinifera [68], Carica papaya [65], Arabidopsis thaliana [10]- [LTR element coverage obtained from 61], Fragaria vesca [66], Malus domestica [61], Glycine max [67], Phaseolus vulgaris (data obtained from phytozome - http://www.phytozome.net/ webcite), Populus trichocarpa [60] - [LTR element coverage obtained from 61], Linum usitatissimum (flax - this study), Ricinus communis [59]. The transposable elements from the genomes of Theobroma cacao [69] and Cucumis sativus [70] have more Copia than Gypsy elements but could not be included in the figure since their actual coverage on the genome was not specified.

Format: DOCX Size: 49KB Download file

Open Data