Open Access Highly Accessed Research article

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Douglas S Domingues14, Guilherme MQ Cruz1, Cushla J Metcalfe1, Fabio TS Nogueira2, Renato Vicentini3, Cristiane de S Alves2 and Marie-Anne Van Sluys1*

  • * Corresponding author: Marie-Anne Van Sluys mavsluys@usp.br

  • † Equal contributors

Author Affiliations

1 GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil

2 Depto. de Genética, Inst. de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000 Botucatu, Brazil

3 Systems Biology Laboratory, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, Brazil

4 Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Rod. Celso Garcia Cid (PR-445), km375, 86047-902 Londrina, Brazil

For all author emails, please log on.

BMC Genomics 2012, 13:137  doi:10.1186/1471-2164-13-137

Published: 16 April 2012

Additional files

Additional file 1:

Gypsy and Copia Maximum Likelihood phylogenies. Maximum-likelihood phylogeny of Gypsy families (Figure 1) based on reverse transcriptase. Sequences from the Gypsy database [8] are denoted with a plus symbol, those from Du et al. [7] with a star. Maximum-likelihood phylogeny of Copia families (Figure 2) based on reverse transcriptase. Sequences from the Gypsy database [8] are denoted with a plus symbol, those from Wicker and Keller [6] with a star. Robustness of the nodes was estimated by 500 bootstrap replications. Bootstrap values below 50 are not shown.

Format: PPTX Size: 101KB Download file

Open Data

Additional file 2:

Fluorescence in situ hybridization with the DEL probe. Figure of fluorescence in situ hybridization using the Del probe, prepared and labelled twice, once with Digoxigenin (DIG) and detected with Anti-DIG-Rhodomine (red signal) and once with Biotin and detected with NeutrAvidin-Oregon Green(green signal). The probes were hybridized to the same slide in consecutive FISH experiments under the same conditions. The same pattern was observed for both probes, suggesting that the signal was real, and the same FISH conditions was used for all LTR-RT probe.

Format: PPTX Size: 1.4MB Download file

Open Data

Additional file 3:

Assignment of previously described cDNA sequences to LTR-RT families. Thirty manually curated sugarcane cDNAs related to LTR-RTs [20] were assigned to a family according Wicker et al. [5]: 80% coverage with 80% nucleotide identity.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 4:

sRNA mapping to individual LTR-RT elements. Mapping of sRNAs within each LTR-RT family (Figures 1 to 7). 20-22nt sRNAs are represented as blue lines, 23-25ntsRNAs as red lines. Each figure shows a different lineage, and includes all the families of that lineage. A scaled schematic (also shown in Figures 1 and 2), is shown below each sRNA map.

Format: PPTX Size: 759KB Download file

Open Data

Additional file 5:

Total 20-22nt and 23-25nt sRNA counts for each LTR-RT family. Total 20-22nt (black) and 23-25nt (grey) sRNA counts for each LTR-RT family, with a mismatch of 2nt allowed.

Format: PPTX Size: 87KB Download file

Open Data

Additional file 6:

LTR-RT information. Name assigned in this paper, pre-existing name from [14,20], GenBank accession number, size of full-length element, length of 5' and 3' LTRs, and sequence of 5 and 3' TSDs, for individual LTR-RT sequences.

Format: XLSX Size: 15KB Download file

Open Data