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Open Access Highly Accessed Research article

Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

Jiří Macas*, Pavel Neumann and Alice Navrátilová

Author Affiliations

Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic

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BMC Genomics 2007, 8:427  doi:10.1186/1471-2164-8-427

Published: 21 November 2007

Additional files

Additional file 1:

Repetitive sequences and their copy number estimates used for the evaluation of repeat representation in 454 data. The table provides GenBank accession numbers, descriptions and experimentally determined copy numbers of selected pea repeats together with calculations of their genomic abundance based on the 454 data.

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Additional file 2:

Sorted list of 50 reconstructed contigs with the highest genome representation.

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Open Data

Additional file 3:

Assignment of clusters of reconstructed contigs to individual repeat families.

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Open Data

Additional file 4:

Phylogenetic analysis of Ty3/gypsy elements based on their reverse transcriptase domains. Phylogenetic trees show relationship of reverse transcriptase domains identified in pea 454 contigs to those from selected plant retroelements. Only contigs bearing complete or marginally truncated (marked with asterisks) RT domains were used for analysis and their names and positions are labeled with yellow boxes. Contigs containing only partial RT sequences were assigned to the trees based on their sequence similarity to full-length domains (labeled as "best hit"). Copy numbers of elements belonging to individual clades are provided in Figure 4.

Format: PDF Size: 89KB Download file

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Open Data

Additional file 5:

Phylogenetic analysis of Ty1/copia elements based on their reverse transcriptase domains. Phylogenetic trees show relationship of reverse transcriptase domains identified in pea 454 contigs to those from selected plant retroelements. Only contigs bearing complete or marginally truncated (marked with asterisks) RT domains were used for analysis and their names and positions are labeled with yellow boxes. Contigs containing only partial RT sequences were assigned to the trees based on their sequence similarity to full-length domains (labeled as "best hit"). Copy numbers of elements belonging to individual clades are provided in Figure 4.

Format: PDF Size: 92KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

PCR primers used for preparation of FISH probes for reconstructed tandem repeats.

Format: PDF Size: 37KB Download file

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Open Data