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Transcriptomic analysis and co-expression network construction in model systems for identification of genes involved in secondary cell wall deposition and lignin metabolism in grasses

Grant number: 16/06917-1
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): March 01, 2017
Effective date (End): November 30, 2019
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Igor Cesarino
Grantee:Sávio de Siqueira Ferreira
Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated research grant:15/02527-1 - Development of model systems in sorghum and a systems biology approach to unravel the molecular mechanisms controlling lignin metabolism in grasses, AP.BIOEN.JP


The production of lignocellulosic biofuels still faces technical difficulties regarding the efficient degradation of plant biomass, which is known as recalcitrance. In order to develop biotechnological strategies to reduce biomass recalcitrance, it is essential to understand the molecular basis of Secondary Cell Wall (SCW) biosynthesis and deposition, since SCW is the main constituent of plant biomass. Although C4 grasses are the main bioenergy crops, most of the knowledge on SCW metabolism has been generated in dicotyledonous plants. These two groups of plants differ considerably in composition, structure and regulation of the cell wall, which hampers the translation from results obtained in dicots to grasses. Thus, the characterization of specific aspects of secondary cell wall metabolism in grasses requires systematic studies in this group of plants. Recently, we started a systems biology study based on metabolomics and transcriptomics in sorghum model systems at Prof. Igor Cesarino's (IB/USP) laboratory to correlate changes in secondary cell wall biochemical compositions with changes in gene expression (Project BIOEN Young Investigator, 2015/02527-1). In this context, the goal of this post-doc project is to analyze the transcriptome of the model systems and generate co-expression networks, in order to identify genes potentially involved in the deposition of secondary cell wall, with a special focus in lignin, and initiate the functional characterization of transcription factors previously chosen based on co-expression networks by transient expression assays. The knowledge generated will be important to develop biotechnological strategies to reduce the recalcitrance of biomass in bioenergy crops such as sugarcane. (AU)

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Scientific publications (5)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
SIMOES, MARCELLA SIQUEIRA; FERREIRA, SAVIO SIQUEIRA; GRANDIS, ADRIANA; RENCORET, JORGE; PERSSON, STAFFAN; FLOH, ENY IOCHEVET SEGAL; FERRAZ, ANDRE; DEL RIO, JOSE C.; BUCKERIDGE, MARCOS SILVEIRA; CESARINO, IGOR. Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming. FRONTIERS IN PLANT SCIENCE, v. 11, . (14/50884-5, 16/50189-0, 15/02527-1, 19/13936-0, 15/18361-5, 16/06917-1, 16/17541-2)
DINIZ, AUGUSTO L.; FERREIRA, SAVIO S.; TEN-CATEN, FELIPE; MARGARIDO, GABRIEL R. A.; DOS SANTOS, JOAO M.; BARBOSA, GERALDO V. DE S.; CARNEIRO, MONALISA S.; SOUZA, GLAUCIA M.. Genomic resources for energy cane breeding in the post genomics era. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, v. 17, p. 1404-1414, . (14/50921-8, 16/06917-1, 15/22993-7, 17/02270-6)
SIMOES, MARCELLA SIQUEIRA; CARVALHO, GABRIEL GARON; FERREIRA, SAVIO SIQUEIRA; HERNANDES-LOPES, JOSE; DE SETTA, NATHALIA; CESARINO, IGOR. Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification. PLANTA, v. 251, n. 2, . (15/02527-1, 16/06917-1, 16/50189-0)
FERREIRA, SAVIO SIQUEIRA; SIMOES, MARCELLA SIQUEIRA; CARVALHO, GABRIEL GARON; ALVES DE LIMA, LEYDSON GABRIEL; DE ALMEIDA SVARTMAN, RAPHAEL MENDES; CESARINO, IGOR. The lignin toolbox of the model grass Setaria viridis. Plant Molecular Biology, v. 101, n. 3, p. 235-255, . (16/06917-1, 16/50189-0, 15/02527-1)
SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, . (13/07467-1, 08/52074-0, 14/50921-8, 15/22993-7, 12/51062-3, 17/02270-6, 11/50761-2, 16/17545-8, 16/06917-1, 13/23048-9, 08/52146-0)

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