Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum
Article first published online: 17 JUN 2014
© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd
The Plant Journal
Volume 79, Issue 1, pages 162–172, July 2014
How to Cite
Grativol, C., Regulski, M., Bertalan, M., McCombie, W. R., da Silva, F. R., Zerlotini Neto, A., Vicentini, R., Farinelli, L., Hemerly, A. S., Martienssen, R. A. and Ferreira, P. C. G. (2014), Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. The Plant Journal, 79: 162–172. doi: 10.1111/tpj.12539
- Issue published online: 24 JUN 2014
- Article first published online: 17 JUN 2014
- Accepted manuscript online: 28 APR 2014 05:00AM EST
- Manuscript Accepted: 8 APR 2014
- Manuscript Revised: 3 APR 2014
- Manuscript Received: 20 AUG 2013
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
- Instituto Nacional de Ciência e Tecnologia em Fixação Biológica de Nitrogênio (INCT)
- Financiadora de Estudos e Projetos (FINEP)
- Fundação de Amparo à Pesquisa do Rio de Janeiro (FAPERJ)
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
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.
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.doc||Word document||53K||Appendix 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.|
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