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Open Access Highly Accessed Research article

Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa

Palitha Dharmawardhana1, Amy M Brunner2 and Steven H Strauss1*

Author Affiliations

1 Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA

2 Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, 24061-0324, USA

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BMC Genomics 2010, 11:150  doi:10.1186/1471-2164-11-150

Published: 4 March 2010

Additional files

Additional file 1:

Core-xylem genes. Populus trichocarpa genes on the array that are homologous to core xylem-predominant genes in Arabidopsis [23].

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Additional file 2:

Differentially expressed genes. Populus trichocarpa genes that were differentially expressed (3016 genes). Gene order as in the Figure 4(A) cluster diagram.

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Additional file 3:

qRT-PCR validation of microarray results. qRT-PCR expression comparison of 9 selected genes from the microarray data; (1) estExt_Genewise1_v1.C_1240151,(2) estExt_Genewise1_v1.C_1700234,(3) gw1.XVI.2910.1,(4) eugene3.00121203,(5) gw1.236.44.1,(6) gw1.IX.897.1,(7) fgenesh4_pg.C_LG_III000388,(8) fgenesh1_pg.C_scaffold_385000002 and (9) estExt_fgenesh4_pm.C_LG_III0736. Genes 1 to 3 are from the gene cluster with high IN9 expression (Figure 4); genes 4 to 6 are from the IN2 high expression cluster, and genes 7 to 9 are from the IN5 high expression cluster. The fold-changes for genes 1 to 3 are between those found for IN9 and IN2, for genes 4 to 6 are between those found for IN2 and IN9 and for genes 7 to 9 are between those found for IN5 and IN2. The error bars on the qRT-PCR data column represent the standard deviation between the averages of the three biological replicates.

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Additional file 4:

Xylem maturation genes. IN5 and IN9 upregulated genes that overlap with initial xylem maturation zone (cryosections MX1: [42]) over expressed genes (log2 expression ratio >2).

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Additional file 5:

Differentially expressed Populus trichocarpa transcription regulators. Gene order as in the Figure 4(B) cluster diagram.

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Additional file 6:

Transcription regulators and vascular development. Literature on transcription factor and regulator classes implicated in vascular and xylem development.

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Additional file 7:

Expression pattern of transcription factor families. Cluster diagram of regulated transcription factor families implicated in vascular and xylem development.

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Additional file 8:

Expression pattern of carbohydrate catalyzing enzymes (CAZyme). Cluster diagrams of expressed CAZyme gene family members: Glycosyl transferases (GTs), glycosyl hydrolases (GHs), polysaccharide lyases (PLs), and carbohydrate esterases (CEs).

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Additional file 9:

Gene identities for Figures 7, 8, 9, 10 and 11. Gene lists, and gene names and/or closest hit information corresponding to Figures 7, 8, 9, 10 and 11. Gene order is as in cluster diagrams.

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Additional file 10:

Microarray replicate correspondences. Scatter plots of intensity values for all differentially expressed genes (FDR < 0.05, 2-fold) between biological replicate sample 1 and replicate sample 2 at each internode.

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Additional file 11:

Primers used for qRT-PCR verification. The sequence, length, tm, GC%, and product sizes of primers used for qRT-PCR.

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