tpj12539-sup-0001-FigS1-S5.docxWord document559K

Figure S1. Workflow with main steps of MF reads assembly.

Figure S2. Venn diagrams with the number of MF scaffolds of each assembly that matched to sugarcane ESTs and RNA-seq reads.

Figure S3. Hits distribution of SOAPdenovo and ABySS+SSPACE scaffolds at the proteins datasets.

Figure S4. Representative diagrams of two MF scaffolds annotated as sucrose phosphate synthase (SPS).

Figure S5. Comparison between the secondary structure of Sof-MIR160 and Sof-MIR398 deposited at miRBase with the hairpin structure obtained with MF scaffolds.

tpj12539-sup-0002-TableS1-S6.docxWord document35K

Table S1. Repeat filtration based on hits comparisons of MF and UF sequences on TIGR_Gramineae database.

Table S2. Gene enrichment factor (FP) calculation based on blast search of MF (Methyl-filtered) and UF (Unfiltered) sequences against sorghum CDS dataset.

Table S3. Summary of number of reads retrieved on each step of assembly pipeline.

Table S4. Summary of number of reads obtained from RNA-seq.

Table S5.Comparisons of assemblies based on hits with sugarcane ESTs and RNA-seq data.

Table S6. Sucrose/starch metabolism genes annotation results of MF scaffolds.

tpj12539-sup-0003-appendixS1.docWord document53KAppendix S1. MF library construction; Curation of the sorghum dataset; Protein set classification; BAC clones source; S. spontaneum and S. officinarum library construction and sequencing; MIRcheck pipeline.
tpj12539-sup-0004-legends.docWord document38K 

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