Open Access Research article

Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties

Marika Vitikainen*, Mikko Arvas, Tiina Pakula, Merja Oja, Merja Penttilä and Markku Saloheimo

Author Affiliations

VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland

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BMC Genomics 2010, 11:441  doi:10.1186/1471-2164-11-441

Published: 19 July 2010

Additional files

Additional file 1:

Mutations identified both in aCGH analysis and sequencing [9]in NG14 and Rut-C30. Strain: the strain(s) in which a mutation has been identified, scaffold: scaffold number, probe start and probe end: coordinates of the probe in which the mutation is seen (probe start is the first probe and probe end is the last probe in which the mutation is seen), gene id: the gene according to the protein id in T. reesei database v2.0 [17]. Gene id is included if a mutation is considered to be located in one of the gene elements: coding region (IN), promoter or terminator. IN exon or IN intron is marked if the site is sequenced. Note that a mutation may affect two genes. Position: the exact coordinate of the mutation if sequenced. Mutation: description of the mutation.

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Additional file 2:

Mutations identified both in aCGH analysis and sequencing [9]in Rut-C30. see Additional file 1.

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Additional file 3:

Position of mutations in probes versus log2 signal. A. Substitutions not detected by aCGH but reported in [9]. B. Substitutions detected both in aCGH and [9]. C. Deletions not detected by aCGH but reported in [9]. D. Deletions detected both in aCGH and [9]. The average probe length of 50 nt was used as the length of probe.

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Additional file 4:

Genes of the 85 kb deletion in the scaffold 15 and classification of genes to categories. Gene identifier number for genome version 2.0 and 1.2, strand, start and end coordinates on scaffold 15, description from [7], whether the [39] protein clustering data set contains a close T. reesei homologue for the gene, whether [37] supplementary table 2c specifies the InterPro identifier as representative for NSBs, whether [39] additional file 2 specifies the InterPro domain as Pezizomycotina enriched, whether [40] supplementary table 1 of subtelomeric genes has the corresponding InterPro identifier, whether [38] supplementary table 11 of overrepresented domains in lineage specific regions has the corresponding InterPro identifier, count of ESTs according to [37] and InterPro domain identifiers found in the protein. As [37] supplementary table 2c has some Interpro identifiers both as NSB and SB representative, the count of identifiers was normalised with the count of genes in NSB and SB regions and only those relatively more abundant in NSBs were considered as NSB representatives. In [39] additional file 2 the Interpro identifiers with a negative value in PC1 were counted as Pezizomycotina enriched. According to [39] dataset gene 109199 has homologues only in Agaricomycotina, Coprinopsis cinerea CC1G_02170 (Uniprot A8NKF5) being the closest.

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