The Sugarcane Transcriptome

We study signaling and regulatory networks in sugarcane and develop tools for a systems biology approach in this grass. As a starting point we intend to characterize three agronomical traits of interest: drought, brix and lignin content.

We are doing an integrated analysis of the sugarcane transcriptome and physiological changes associated to sucrose content, stress responses and fiber quality and content. We would like to be able to alter carbon partition in this crop to generate an energy grass. As a starting point sugarcane metabolic pathways are being mapped in conjunction with the transcriptome data.

We are focusing on the study of gene categories with a well known regulatory role (Transcription Factors, Protein Kinases and Phosphatases), producing transgenics and developing a database and computacional tools to integrate the several levels of information.

Cia, Mariana Cicarelli ; Carvalho, Giselle ; Azevedo, Ricardo Antunes ; Monteiro-Vitorello, Claudia Barros ; Souza, Glaucia Mendes ; Nishiyama-Júnior, Milton Yutaka ; Lembke, Carolina Gimiliani ; Faria, Raphael S.C.A. ; Marques, João Paulo Rodrigues ; Melotto, Maeli ; Camargo, Luis Eduardo Aranha . Novel insights into the early stages of ratoon stunting disease of sugarcane inferred from transcript and protein analysis. Phytopathology, v. 1, p. 1-58, 2018.

Tavares, EQP ; Grandis, A ; Lembke, CG ; Souza, GM ; Purgatto, E ; de Souza, AP ; Buckeridge, MS . Roles of Auxin and Ethylene in Aerenchyma Formation in Sugarcane Roots. Plant Signalling & Behavior (Online), v. 1, p. 00-00, 2017.

Cunha, Camila P. ; Roberto, Guilherme G. ; Vicentini, Renato ; Lembke, Carolina G. ; Souza, Glaucia M. ; Ribeiro, Rafael V. ; Machado, Eduardo C. ; Lagôa, Ana M. M. A. ; Menossi, Marcelo . Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening. Scientific Reports, v. 7, p. 43364, 2017.

Ferreira, S. S., Hotta, C. T., Poelking, V. G. C., Leite, D. C. C., Buckeridge, M. S., Loureiro, M. E., Barbosa, M. H. P., Carneiro, M. S., Souza, G. M. (2016). Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. Plant Molecular Biology 1-21. 10.1007/s11103-016-0434-2.

Moraes, I., Yuan, Zuo-Fei., Liu, S., Souza, G. M., Garcia, B. A., Casas-Mollano, J. A. (2015). Analysis of histones H3 and H4 reveals novel and conserved post-translational modifications in sugarcane. PLOS ONE, v. 10, p. e0134586.

Gentile, A., Ferreira, T. H., Mattos, R. S., Dias, L. I., Hoshino, A. A., Carneiro, M. S., Souza, G. M., Calsa, T., Nogueira, R. M., Endres, L., Menossi, M. (2013). Effects of drought on the microtranscriptome of field-grown sugarcane plants. Planta Heidelberg, v. 3, p. 783-798.

Hotta, C. T., Nishiyama Jr, M. Y., Souza, G. M. (2013). Circadian rhythms of sense and antisense transcription in Sugarcane, a highlypolyploid crop. PLOS ONE 2013 8(8) doi:10.1371/journal.pone.0071847.

Lembke, C. G., Nishiyama-Jr, M. Y., Sato, P. M., Andrade, R. F., Souza, G. M. (2012). Identification of sense and antisense transcripts regulated by drought in sugarcane. Plant Molecular Biology. 79, 461.

Begcy, K., Mariano, E. D., Gentile, A., Lembke, C. G., Souza, G. M., Menossi, M. (2012) A novel stress-induced sugarcane gene confers tolerance to drought, salt and oxidative stress in transgenic tobacco plants. PLOS ONE 7(9): e44697. doi:10.1371/journal.pone.0044697. www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044697.

Costa, M. D-B. L, Hotta, C. T., Carneiro, M. S., Chapola, R. G., Hoffmann, H. P., Garcia, A. A. F., Souza, G. M.  (2011). Sugarcane Improvement: How far can we go? Current Opinion in Biotechnology 23:1–6.

Waclawovsky, A.J., Sato, P. M., Lembke, C. G., Moore, P. H and Souza, G. M. (2010). Sugarcane for Bioenergy Production: an assessment of yield and regulation of sucrose content. Plant Biotechnology Journal 8, 1-14. doi: 10.1111/j.1467-7652.2009.00491.x

Papini-Terzi, F. S., Rocha, F. R., Vêncio, R. Z. N., Felix, J. M., Branco, D., Waclawovsky, A. J., Del-Bem, L. E. V., Lembke, C. G., Costa, M. D-B. L., Nishiyama-Jr, M. Y., Vicentini, R., Vincentz, M., Ulian, E. C., Menossi, M., Souza, G. M. (2009). Genes associated with sucrose content. BMC Genomics 10, 120. doi:10.1186/1471-2164-10-120

Felix, J. M., Papini-Terzi, F. S., Rocha, F. R., Vêncio, R. Z. N., Vicentini, R., Nishiyama-Jr, M. Y., Ulian, E. C., Souza, G. M. and Menossi, M. (2009). Expression profile of signal transduction components in a sugarcane population segregating for sugar content. Tropical Plant Biology. DOI 10.1007/s12042-009-9031-8

Menossi, M., Silva-Filho, M. C., Vincentz, M. Van-Sluys, M. A. e Souza, G. M.  (2008). Sugarcane Functional Genomics: gene discovery for agronomic trait development. Int. J. Plant Genomics (eprint 2008:458732).

Souza, A. P., Gaspar, A., Silva, E. A., Ulian, E., Waclawovsky, A. J., Nishiyama-JR., M. Y., Vicentini, R., Menossi, M., Souza, G. M., and Buckeridge, M. (2008). Elevated CO2 induces increases in photosynthesis, biomass, productivity and modifies gene expression in sugarcane. Plant Cell & Environment 31, 1116-27.

Rocha, F. R., Papini-Terzi, F. S., Nishiyama-Jr, M. Y., Vêncio, R. Z. N., Vicentini, R., Duarte, R. D. C., Rosa-Jr, V. E., Vinagre, F., Barsalobres, C., Medeiros, A. H., Rodrigues, F. A., Ulian, E. C., Zingaretti, S. M., Galbiatti, J. A., Almeida, R. S., Figueira, A. V. O., Hemerly, A. S., Silva-Filho, M. C., Menossi, M. and Souza, G. M. Signal transduction-related responses to phytohormones and environmental challenges in sugarcane. (2007). BMC Genomics 8, 71.

Papini-Terzi, F. S., Rocha, F. R., Vêncio, R. Z. N., Oliveira, K. C., Felix, J. M., Vicentini, R., Rocha, C. S., Simões, A. C. Q., Ulian, E. C., di Mauro, S. M. Z., da Silva, A. M., Pereira, C. A. B., Menossi, M. and Souza, G. M. (2005). Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Research 12, 27-38.

Souza, G. M., Simoes, A. C. Q. Oliveira, K. C., Garay, H. M.,  Fiorini, L. C., Gomes, F. S.,  Nishiyama-Junior, M. Y. and da Silva, A. M. (2001). The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane. Genet. Mol. Biol. 24, 25-34.