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Open Access Research article

Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola

Jun-Jun Liu*, Rona N Sturrock and Ross Benton

Author Affiliations

Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1 M5, Canada

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BMC Genomics 2013, 14:884  doi:10.1186/1471-2164-14-884

Published: 16 December 2013

Additional files

Additional file 1:

Table S1. RNA-seq reads generated and analyzed in three pooled western white pine primary needles. Table S2. BLAST search to evaluate transcriptome data sets of western white pine primary needles. Table S3. Top ten sequences with most abundant expression levels based on total gene reads or their RPKM values. Table S4. Gene and enzyme numbers of metabolic pathways detected in the whole primary needle transcriptome and differentially expressed genes (DEGs) regulated in the white pine-blister rust (WP-BR) interactions.

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Additional file 2: Figure S1:

Plot analysis of transcript expression values (RPKM) in three western white pine cDNA libraries for quality control. The RPKM overall distribution and variability of three cDNA libraries/samples were similar, indicating that they were comparable for identification of differentially expressed genes (DEGs) at the transcriptome level. (A) A box plot analysis using CLC genomics work bench; (B) A density plot using Bioconductor (version 2.12) software in conjunction with R software (version 3.0.0).

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Additional file 5:

Table S13. Functional grouping of differentially expressed genes (DEGs) during early stages of compatible and incompatible white pine-blister rust (WP-BR) interactions. Table S14. A list of contigs used in the K-means clustering analysis. Table S15. A list of primers used for quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR).

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Additional file 3: Figure S2:

Functional classification of the differentially expressed genes (DEGs) in white pine-blister rust (WP-BR) interactions at an early stage (4-dpi) post Cronartium ribicola inoculation. Subcategories (A) for biological process (BP), (B) for molecular function (MF), and (C) for cellular component (CC).

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Additional file 4:

Table S5. A list of 245 contigs with significant up-regulation specifically in resistant (Cr2/ -) seedling post C. ribicola infection (4-dpi). Table S6. A list of 142 contigs with significant down-regulation specifically in resistant (Cr2/ -) seedling post C. ribicola infection (4-dpi). Table S7. A list of 114 contigs with significant up-regulation specifically in susceptible (cr2/cr2) seedling post C. ribicola infection (4-dpi). Table S8. A list of 46 contigs with significant down-regulation specifically in susceptible (cr2/cr2) seedling post C. ribicola infection (4-dpi). Table S9. A list of 204 contigs with significant up-regulation in both resistant (Cr2/ -) and susceptible (cr2/cr2) seedling post C. ribicola infection (4-dpi). Table S10. A list of 106 contigs with significant down-regulation in both resistant (Cr2/ -) and susceptible (cr2/cr2) seedling post C. ribicola infection (4-dpi). Table S11. A list of 141 contigs with significantly higher expression levels in resistant (Cr2/ -) seedlings than in susceptible (cr2/cr2) seedling post C. ribicola infection (4-dpi). Table S12. A list of 134 contigs with significantly higher expression levels in susceptible (cr2/cr2) seedling than in resistant (Cr2/ -) seedlings post C. ribicola infection (4-dpi).

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