Open Access Highly Accessed Research article

Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

Nicolas Blavet1*, Delphine Charif2, Christine Oger-Desfeux3, Gabriel AB Marais2 and Alex Widmer1

Author Affiliations

1 Institute of Integrative Biology (IBZ), ETH Zurich, Universitaetstrasse 16, Zürich, 8092, Switzerland

2 Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, F-69622 cedex, France

3 DTAMB/PRABI, IFR41, Université Lyon 1, Bâtiment Gregor Mendel, Villeurbanne, F-69622 cedex, France

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BMC Genomics 2011, 12:376  doi:10.1186/1471-2164-12-376

Published: 26 July 2011

Additional files

Additional file 1:

Distribution of ESTs per unigene. Distribution of EST reads per unigene in the SlF library. The x-axis represents EST reads per unigene and the y-axis the number of unigenes.

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Additional file 2:

Highly expressed genes. Fifteen genes were identified among the ten most strongly expressed genes in each library. The two first genes coding for homologues of alpha-tubulin and an unknown gene in Pinus koraiensis are present in at least four of our libraries. 'Presence' indicates the number of libraries in which a given gene was found among the ten most strongly expressed genes. E-value cut-off 1E-4.

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Additional file 3:

Relative frequencies of the most represented Molecular Function GO sub-classes across libraries. Additional Figure 2 shows the 10 most frequent molecular function GO terms at level 3 in the five species Silene latifolia, S. dioica, S. marizii, S. vulgaris and Dianthus superbus.

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Additional file 4:

BLAST hits of unigenes in the eight individual libraries with different databases. BLAST hits of unigenes in the eight individual libraries with the following databases (E-value cut-off 1E-4): AT = Arabidopsis thaliana, VV = Vitis vinifera, PT = Populus trichocarpa, SL = Silene latifolia. Protein sequences were downloaded from: http://plants.ensembl.org/info/data/ftp/index.html webcite: AT proteome = TAIR10.pep 07.02.2011, VV proteome = IGGP12x.pep 07.02.2011, PT proteome = JGI2.0.pep 07.02.2011. AT EST = AGI_release_15, VV EST = VVGI_release_7, PT EST = PPLGI_release_5. SL mtDNA is S. latifolia mtDNA described in (Sloan et al., 2010). Uniprot release 07.2010. A. thaliana mtDNA, cpDNA, exon, intron, intergenic, 3' UTR and 5' UTR come from TAIR10.

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