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

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 pathways involving differentially expressed genes after <i>S. scitamineum</i> inoculation in “ROC”22.

<p>Notes: T2 <i>vs.</i> T1, T3 <i>vs.</i> T1 and T4 <i>vs.</i> T1 =  combination of “ROC”22 sample under <i>S. scitamineum</i> stress for 24, 48, or 120 h and Yacheng05-179 under sterile water stress after 24 h, respectively.</p><p>Analysis of pathways involving differentially expressed genes after <i>S. scitamineum</i> inoculation in “ROC”22.</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

Cluster heatmap of expression patterns of differentially co-expressed genes in both sugarcane cultivars at different time points after <i>S. scitamineum</i> inoculation.

<p>T1, T2, T3 and T4 denote “ROC”22 at 24 h after water inoculation, and at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation, respectively; 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; k1∼k9 indicate nine distinct expression patterns of differentially co-expressed genes.</p

Dynamic expression models of differentially expressed genes in “ROC”22 after <i>S. scitamineum</i> inoculation (T1→T2→T3→T4).

<p>T1, T2, T3 and T4 denote “ROC”22 at 24 h after water inoculation, and at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation, respectively.</p

RT-qPCR validation of parts of differentially expressed genes identified by Illumina sequencing.

<p>Q1, metacaspase-1-like gene; Q2, ribonuclease 3-like gene; Q3, pathogenesis-related protein (PR-10) gene; Q4, sucrose transporter (SUT1) gene; Q5, vacuolar amino acid transporter 1-like gene; Q6, heat shock protein-like gene. Y, Yacheng05-179; R, “ROC”22; 24 h, 48 h and 120 h, sugarcane buds inoculation with <i>Sporisorium scitamineum</i> at 24 h, 48 h and 120 h, respectively; qPCR, detection results of real-time fluorescent quantitative PCR; log₂FC, fold change of the differential expression genes in the transcriptome.</p

Venn diagram of differentially co-expressed genes in both sugarcane cultivar after <i>S. scitamineum</i> inoculation at different time points.

<p>DR24, DR48 and DR120 denote differentially expressed gene sets obtained from “ROC”22 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample at 24 h after water inoculation, respectively; DY24, DY48 and DY120 denote differentially expressed gene sets obtained from Yacheng05-179 samples at 24, 48 and 120 h after <i>S. scitamineum</i> inoculation compared to control sample at 24 h after water inoculation, respectively; All DEGs, all differentially expressed genes; Up-regulation DEGs, up-regulated genes; Down-regulation DEGs, down-regulated genes.</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