Open Access Highly Accessed Research article

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

Sukhjiwan Kaur1, Luke W Pembleton1, Noel OI Cogan1, Keith W Savin1, Tony Leonforte2, Jeffrey Paull4, Michael Materne2 and John W Forster13*

Author Affiliations

1 Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia

2 Department of Primary Industries, Biosciences Research Division, Grains Innovation Park, Horsham, Victoria 3401, Australia

3 La Trobe University, Bundoora, Victoria 3086, Australia

4 School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia

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BMC Genomics 2012, 13:104  doi:10.1186/1471-2164-13-104

Published: 20 March 2012

Additional files

Additional file 1:

Consensus sequences of assembled contigs from field pea. The data represents the consensus sequences of 13,602 assembled contigs generated as a result of de novo assembly of field pea ESTs.

Format: TXT Size: 10.5MB Download file

Open Data

Additional file 2:

Sequence information on singletons from field pea. The data represents the sequence information on all the singletons generated from de novo assembly of field pea ESTs.

Format: TXT Size: 18.3MB Download file

Open Data

Additional file 3:

Consensus sequences of assembled contigs from faba bean. The data represents the consensus sequences of 6,370 assembled contigs generated as a result of de novo assembly of faba bean ESTs.

Format: TXT Size: 4.2MB Download file

Open Data

Additional file 4:

Sequence information on singletons from faba bean. The data represents the sequence information on all the singletons generated from de novo assembly of faba bean ESTs.

Format: TXT Size: 15.8MB Download file

Open Data

Additional file 5:

Bioinformatic annotation (BLASTN) of field pea unigene set against the Medicago truncatula genome. This file contains the BLAST results obtained as a result of comparison of field pea unigene set against the M. truncatula genome at an E value < 10-10.

Format: XLS Size: 2.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Bioinformatic annotation (BLASTX) of field pea unigene set against the nr database of GenBank. This file contains the BLAST results obtained as a result of comparison of field pea unigene set against the GenBank nr database at an E value < 10-10.

Format: XLS Size: 9.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Bioinformatic annotation (BLASTN) of field pea unigene set against the Arabidopsis thaliana genome. This file contains the BLAST results obtained as a result of comparison of field pea unigene set against the A. thaliana genome at an E value < 10-10.

Format: XLS Size: 1.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Bioinformatic annotation (BLASTN) of faba bean unigene set against the Medicago truncatula genome. This file contains the BLAST results obtained as a result of comparison of faba bean unigene set against the M. truncatula genome at an E value < 10-10.

Format: XLS Size: 2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Bioinformatic annotation (BLASTX) of faba bean unigene set against nr database of GenBank. This file contains the BLAST results obtained as a result of comparison of faba bean unigene set against the GenBank nr database at an E value < 10-10.

Format: XLS Size: 7.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

Bioinformatic annotation (BLASTN) of faba bean unigene set against Arabidopsis thaliana genome. This file contains the BLAST results obtained as a result of comparison of faba bean unigene set against the A. thaliana genome at an E value < 10-10.

Format: XLS Size: 1.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Bioinformatic annotation (BLASTN) of field pea and faba bean unigene sets against the Glycine max genome. This file contains the BLAST results obtained as a result of comparison of field pea and faba bean unigene sets against G. max genome at an E value < 10-10.

Format: XLS Size: 6.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

Bioinformatic annotation (BLASTN) of field pea and faba bean unigene sets against the Pisum sativum transcriptome dataset from Franssen et al 2011. This file contains the BLAST results obtained as a result of comparison of field pea and faba bean unigene sets against P. sativum transcriptome dataset at an E value < 10-10.

Format: XLS Size: 10MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 13:

BLASTN of field pea and faba bean contigs and singltones against GenBank EST and nucleotide (nt) data. This file contains the BLASTN results obtained as a result of comparison of field pea and faba bean contigs and singletons set against the EST and nucleotide (nt) databse of GenBank at an E value < 10-10.

Format: XLSX Size: 7MB Download file

Open Data

Additional file 14:

Sequence information of all of the SSR primer pairs identified and designed using BatchPrimer3 from field pea and faba bean ESTs. This file contains all of the information (sequence information, orientation, sequence length, expected product length, Tm, GC content and SSR motif length) on SSR primer pairs designed using BatchPrimer 3.

Format: XLS Size: 1.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 15:

Characterisation of a sub-sets of EST-SSRs on wild and cultivated genotypes of field pea and faba bean. This file represents the data on number and size of alleles amplified from screening of subsets of EST-SSRprimer pairs on different genotypes of field pea and faba bean.

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data