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Open Access Research article

A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings

Thomas Müller1, Ingo Ensminger23* and Karl J Schmid1*

Author Affiliations

1 Department of Crop Biodiversity And Breeding Informatics, University of Hohenheim, Stuttgart, Germany

2 Department of Biology, University of Toronto at Mississauga, Mississauga, ON, Canada

3 Forest Research Institute of Baden-Württemberg (FVA), Freiburg i. Brsg., Germany

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BMC Genomics 2012, 13:673  doi:10.1186/1471-2164-13-673

Published: 28 November 2012

Additional files

Additional file 1:

Characteristics of the libraries. Number of reads and average read length per library before and after the pre-processing steps.

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Open Data

Additional file 2:

Read composition of the assembly. The origin as well as the number of reads assembled or otherwise marked by Newbler is illustrated.

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Additional file 3:

Log-log plot of assembled reads versus the sequence length. The log-log plot shows that the sequence length is depending on the number of reads assembled to the sequence.

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Open Data

Additional file 4:

Number of isotigs per sequence length. Number of isotigs per sequence length. Reads of all twelve cDNA libraries were assembled using Newbler.

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Open Data

Additional file 5:

Comparison of the GO-Slim categories level 3 - 5. Comparison of the distribution of the GO-Slim categories of the Douglas-fir PUTs set versus Picea sitchensis and Arabidopsis thaliana at GO level 3 to 5. Transcriptome data of P. sitchensis and A. thaliana were obtained from NCBI and TAIR databases, respectively (See text for details).

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Open Data

Additional file 6:

Number of identical BLASTX hits of different combination of groups after the keyword search. This table lists the number of identical BLASTX hits of different combination of groups after the keyword search. If combinations of sets are not listed, there were no equal BLASTX hits.

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Open Data

Additional file 7:

BLASTX keyword search results. This file lists in a tab separated style for each BLASTX keyword search hit the following informations: keyword, isotig id, isotig group, hit id, hit definition, e-value. If there were more than one hit per keyword and isotig, only the best hit (i.e. the one with the smallest e-value) is listed.

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Additional file 8:

Schematic example of Newbler output. Schematic example of contigs, isotigs, and isogroups produced by Newbler.

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Open Data

Additional file 9:

Composition of the cDNA libraries in detail. Two tables describe the cDNA libraries and the provenances in detail.

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Open Data