Comparison of the expression stability of 13 reference genes in <i>Saccharum officinarum</i> as calculated by geNorm, Normfinder and deltaCt.

<p>*β-actin,</p><p>**β-tubulin.</p

Dynamic expression patterns of differentially expressed genes in “ROC”22 after <i>S. scitamineum</i> inoculation.

<p>Notes: 0, 1, 2, 3, <b>−</b>1, <b>−</b>2 and <b>−</b>3 do not refer to the actual expression of the differentially expressed genes, but for the classification mark of gene dynamic changes. Gene numbers represent the actual number of dynamic expression patterns of differentially expressed genes. T1, “ROC”22 sample under sterile water stress after 24 h; T2–T4, “ROC”22 sample under <i>S. scitamineum</i> stress for 24, 48, and 120 h, respectively.</p><p>Dynamic expression patterns of differentially expressed genes in “ROC”22 after <i>S. scitamineum</i> inoculation.</p

Analysis of GO classifications involving differentially co-expressed genes in three models of distinct and notable dynamic expression patterns in both sugarcane genotypes.

<p>Analysis of GO classifications involving differentially co-expressed genes in three models of distinct and notable dynamic expression patterns in both sugarcane genotypes.</p

Venn diagram showing the number of genes with sustained differential co-expression between both sugarcane cultivars.

<p>DR-up and DR-down denote continuously up-regulated/down-regulated gene sets in “ROC”22 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample 24 h after water inoculation, respectively; DY-up and DY-down denote continuously up-regulated/down-regulated gene sets in Yacheng05-179 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample 24 h after water inoculation, respectively.</p

Assembly results of sugarcane transcriptome using trinity software.

<p>Notes: N50 length is an indicator of measuring assembly effect, which is calculated by the accumulated length of the assembled fragments from long to short. When the sum is greater than or equal to 50% of the total length, the final accumulated fragment length is the N50 value. Mean length = for the average assembly length.</p><p>Assembly results of sugarcane transcriptome using trinity software.</p

Dynamic expression models of differentially expressed genes in Yacheng05-179 after <i>S. scitamineum</i> inoculation (T5→T6→T7→T8).

<p>T5, T6, T7 and T8 denote Yacheng05-179 at 24 h after water inoculation, and at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation, respectively.</p

The optimal number of reference genes required for effective normalization in each of four experimental sets in sugarcane.

<p>The pairwise variation (V_n/V_n+1) was analyzed between normalization factors NF_n and NF_n+1 by geNorm program to determined the optimal number of reference genes for accurate normalization in samples from different sugarcane cultivar samples (1^st set), sugarcane hormone-treated (2^nd set), abiotic-treated (3^rd set) and treatments (hormone-& abiotic-treated, 4^th). <i>ACT</i> stand for “β-actin” and <i>TUB</i> stand for “β-tubulin”.</p

Dynamic expression patterns of differentially expressed genes in Yacheng05-179 after <i>S. scitamineum</i> inoculation.

<p>Notes: 0, 1, 2, 3, −1, −2 and −3 do not refer to the actual expression of the differentially expressed genes, but for the classification mark of gene dynamic changes. Gene numbers represent the actual number of dynamic expression patterns of differentially expressed genes. T5, Yacheng05-179 sample under sterile water stress after 24 h; T6–T8, Yacheng05-179 samples under <i>S. scitamineum</i> stress for 24, 48, and 120 h, respectively.</p><p>Dynamic expression patterns of differentially expressed genes in Yacheng05-179 after <i>S. scitamineum</i> inoculation.</p

Expression of resistance-related genes in sugarcane after <i>S. scitamineum</i> infection.

<p>Notes: T2 <i>vs.</i> T1, T3 <i>vs.</i> T1 and T4 <i>vs.</i> T1 refer to a combination of “ROC”22 under <i>S. scitamineum</i> stress for 24, 48, or 120 h and “ROC”22 under sterile water stress after 24 h, respectively. T6 <i>vs.</i> T5, T7 <i>vs.</i> T5 and T8 <i>vs.</i> T5 refer to the combination of Yacheng05-179 under <i>S. scitamineum</i> stress for 24 h, 48 h or 120 h and Yacheng05-179 under sterile water stress after 24 h, respectively.</p><p>Expression of resistance-related genes in sugarcane after <i>S. scitamineum</i> infection.</p

Expression levels and variation of 13 reference genes across four experimental sets in <i>Saccharum officinarum.</i>

<p>Mean Ct value (Mean), Standard deviation (SD) and Covariance (CV) were calculated by Microsoft Excel 2003. 1^st set: leaf, leaf sheath, stem epidermis,stem pith and bud from “ROC”20, “ROC”22, FN40, liucheng03-182 and YC05-179; 2^nd set: ABA, MeJA and SA, treated-samples from “ROC”20, FN40, Liucheng03-182 and YC05-179; 3^rd set: H₂O₂, NaCl, PEG, CuCl₂ and CdCl₂ treated-samples from “ROC”20, FN40, liucheng03-182 and YC05-179; 4^th set: 2ⁿset+3^rd set.</p