Open Access Highly Accessed Research article

Small RNAs, DNA methylation and transposable elements in wheat

Dario Cantu1, Leonardo S Vanzetti12, Adam Sumner1, Martin Dubcovsky3, Marta Matvienko4, Assaf Distelfeld1, Richard W Michelmore14 and Jorge Dubcovsky1*

Author Affiliations

1 Department of Plant Sciences, University of California Davis, One Shields Ave, Davis, CA, USA

2 Grupo de Biotecnología y Rec. Genéticos, INTA EEA Marcos Juárez, Ruta 12 S/N, (2580) Marcos Juárez, Córdoba, Argentina

3 Department of Physics, University of California Davis, One Shields Ave, Davis, CA, USA

4 Genome Center, University of California Davis, One Shields Ave, Davis, CA, USA

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BMC Genomics 2010, 11:408  doi:10.1186/1471-2164-11-408

Published: 29 June 2010

Additional files

Additional file 1:

Figure S1 - sRNA counts in TE families. Box plots represent the distribution of the total counts of sRNA perfectly matching wheat TEs of each family in the seven major superfamilies deposited in the TREP database. Numbers above the whiskers represent the number of TREP elements within each superfamily considered. Figure S2 - LTR length in Copia and Gypsy TEs. Box plots represent the distribution of LTR lengths in the Copia and Gypsy elements deposited in the TREP database. Table S1 - Summary of sRNA libraries. Table S2 - Distribution of sRNA counts in the EU835198 genomic region (T. turgidum). Table S3 - Distribution of sRNA counts in the DQ871219 genomic region (T. turgidum). Table S4 - Distribution of sRNA counts in the EF540321 genomic region (T. turgidum). Table S5 - Distribution of sRNA counts in the EF567062 genomic region (T. aestivum). Table S6 - Distribution of sRNA counts in the DQ537335 genomic region (T. aestivum). Table S7 - sRNA counts in the different TE families. Table S8 - Estimates of LTR age of insertion and cytosine methylation in the CG, CHG, and CHH contexts.

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Open Data

Additional file 2:

dbmanager.py - python program for sRNA database setup.

Format: PY Size: 7KB Download file

Open Data

Additional file 3:

scanner.py - python program for scrolling window analysis with frame size between 18 and 33 nt that scans through the entire query sequence with a 1 nt increment after each read.

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Open Data

Additional file 4:

srna_seeker.py - program for scanning nucleotide sequences for perfect matching sRNAs using "dbmanager.py" to access the sRNA database and "scanner.py" to analyze the query sequences.

Format: PY Size: 7KB Download file

Open Data

Additional file 5:

Cmet_scan.py - python program for counting mutations in potentially methylated sites.

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Open Data