Genes, genomes & transposable elements contribution to plant-microbe interaction: a sugarcane study case

• Grant number: 16/17545-8
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• Start date: October 01, 2017
• End date: April 30, 2025
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Marie-Anne Van Sluys
• Grantee: Marie-Anne Van Sluys
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Pesquisadores principais: Claudia Barros Monteiro Vitorello ; Luis Eduardo Aranha Camargo ; Silvana Aparecida Creste Dias de Souza
• Associated researchers: Fabricio Martins Lopes ; Silvana Aparecida Creste Dias de Souza
• Associated research grant(s): 18/16543-7 - Multi-user equipment 2016/17545-8: fluorescent microscope, AP.EMU; 18/10746-3 - Multi-user equipment 2016/17545-8: real time PCR quantstudio 7 flex, AP.EMU
• Associated scholarship(s): 24/14868-7 - Curating in the assembly and annotation of bacterial genomes, BP.TT; 24/04412-6 - Identification of protein structures using AlphaFold on plant-microorganism transcriptome data., BP.TT; 23/08813-2 - Detection of long non-coding RNAs and analysis of the expression microbiome expression profile in the total transcriptome of sugarcane under biotic stress, BP.DD; + associated scholarships 22/09130-3 - Characterization of new viral particule found in strain of phytopathoenic bacteria, Xanthomonas albilineans, BP.MS; 23/03850-7 - Influence of biotic stress on the sugarcane microbiome, BP.IC; 22/10296-3 - Plant-microbe interaction: an integrative omics view, BP.PD; 22/09736-9 - Analysis of sugarcane gene co-expression networks after microbial infection, BP.TT; 22/09923-3 - Plant and microbe molecular and in vitro growth experimental training., BP.TT; 22/06109-3 - Analysis and comparison of multiple sugarcane metabolic networks to unravel mechanisms of sugarcane immune system, BP.PD; 21/13293-2 - Omics contribution to plant-microbe interaction, BP.PD; 20/11630-9 - Long non-coding RNA and transposable elements in plant microbe interaction, BP.TT; 19/08239-9 - Functional studies of THI1 in plants, BP.DD; 19/05424-0 - In vitro comparative biology of four Xathomonas aeblineans strains, BP.IC; 18/24646-0 - Genome comparative analysis of four Xanthomonas albilineans isolates and prospection of target genes for association studies with known phenotypes, BP.DD; 18/23646-7 - GEMAC target gene annotation and data integration, BP.TT; 18/21693-8 - Detection and quantification of sugarcane diseases in plants indexed for major systemic pathogens, BP.TT; 18/10351-9 - TaqMan assay development to quantify Leifsonia xyli subsp. xyli, Xanthomonas albilineans and Gluconacetobacter diazotrophicus in sugarcane, BP.TT; 18/07615-4 - Studying the first cell communication signals between sugarcane and pathogens: focus on Reactive Oxygen Species., BP.PD; 18/04555-0 - RGAs sugarcane expression profile during infection with various pathogens, BP.PD; 18/02156-1 - Arabidopsis thaliana as a plant model to study plant pathogen interaction between Sporisorium scitamineum and sugarcane, BP.MS; 17/23113-6 - Exploring the molecular cross-talk of the biotrophic pathogen Sporisorium scitamineum and its host sugarcane: the use of Arabidopsis as a model system, BE.PQ; 17/21880-0 - Uncovering the interaction of the bacteria Xanthomonas albilineans and Gluconacetobacter diazotrophicus with the sugarcane endophytic microbiome, BP.PD - associated scholarships

Abstract

Plant-Microbe interaction is a fundamental process in the biosphere that impacts natural ecosystems as well as agroecosystems. The understanding of the biological components and processes that control this interaction is expected to improve crop productivity and monitor environmental quality. Our approach to tackle this complex system is to use genome-wide molecular and bioinformatic tools to uncover key genes that control and/or mediate the interaction of sugarcane with three pathogens (Leifsonia xyli subsp. xyli; Xanthomonas albilineans; Sporisorium scitamineum) and a nitrogen fixing bacteria (Gluconacetobacter) considered to be beneficial to sugarcane. Those organisms have a biotrophic interaction with sugarcane and the molecular aspects under biotrophy/hemibiotrophic are generally less understood. We aim to compare and contrast molecular responses across the individual interactions on both the host and on the microorganisms. Specifically, we will (i) focus on the expression patterns of a previously identified collection of resistance gene analogs (RGA) of sugarcane as well as of genes of specific metabolic responses involved in microbe interactions such as reactive oxygen species (ROS), carbohydrate metabolism, hormone synthesis and regulation, transposable elements genes, and a gene family related to gene editing in organelles and known to have members that are involved in the regulation of plant defenses via Nat- siRNA (pentatricopeptide); (ii) evaluate and compare across species the expression patterns of microbial genes with a particular focus on their secreted molecules among which one is expected to find effectors ; (iii) evaluate and compare changes in the expression patterns during two mixed infections, and (iv) evaluate and compare changes in the microbiome of the host as a result of the interaction with the mentioned microbes. As outreach products, we expect to deliver molecular information on the biology of sugarcane when interacting with various microbes looking forward to the development of a diagnostic kit to monitor sugarcane fields and to build a comprehensive sugarcane phytobiome database that could be used in comparative studies with other Poaceae. (AU)

Scientific publications

(21)

(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)

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, DEC 2019. (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)

TEIXEIRA-SILVA, NATALIA SOUSA; CARVALHO SCHAKER, PATRICIA DAYANE; SILVA RODY, HUGO VIANNA; MAIA, THIAGO; GARNER, CHRISTOPHER M.; GASSMANN, WALTER; MONTEIRO-VITORELLO, CLAUDIA BARROS. Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. JOURNAL OF FUNGI, v. 6, n. 4, DEC 2020. (17/13268-2, 18/04555-0, 16/04429-0, 16/16376-8, 17/25477-5, 16/17545-8, 13/25599-2)

RODY, HUGO V. S.; CAMARGO, LUIS E. A.; CRESTE, SILVANA; VAN SLUYS, MARIE-ANNE; RIESEBERG, LOREN H.; MONTEIRO-VITORELLO, CLAUDIA B.. Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection. FRONTIERS IN PLANT SCIENCE, v. 12, AUG 19 2021. (18/04555-0, 19/13530-4, 16/17545-8)

PARTIDA, VANIA GABRIELA SEDANO; DIAS, HENRIQUE MOURA; CORCINO, DIANA SUSANA MARTINEZ; VAN SLUYS, MARIE-ANNE. Sucrose-phosphate phosphatase from sugarcane reveals an ancestral tandem duplication. BMC PLANT BIOLOGY, v. 21, n. 1, JAN 7 2021. (16/17545-8, 18/10746-3)

BENEVENUTO, JULIANA; TEIXEIRA-SILVA, NATALIA S.; KURAMAE, EIKO E.; CROLL, DANIEL; MONTEIRO-VITORELLO, CLAUDIA B.. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. FRONTIERS IN MICROBIOLOGY, v. 9, APR 6 2018. (17/13268-2, 16/03768-5, 16/16376-8, 16/17545-8, 14/21802-0)

ISHIDA, JULIANE K.; BINI, ANDRESSA P.; CRESTE, SILVANA; VAN SLUYS, MARIE-ANNE. Towards defining the core Saccharum microbiome: input from five genotypes. BMC Microbiology, v. 22, n. 1, p. 16-pg., 2022-08-08. (16/17545-8, 18/07615-4)

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, p. 18-pg., 2019-12-01. (14/50921-8, 08/52074-0, 15/22993-7, 08/52146-0, 12/51062-3, 13/07467-1, 17/02270-6, 11/50761-2, 13/23048-9, 16/06917-1, 16/17545-8)

PERES BINI, A.; SERRA, M. C. D.; SILVA, H. R. V.; RAGAGNIN, G. T.; VITORELLO, C. B. M.; CAMARGO, L. E. A.; VAN SLUYS, M. A.; CRESTE, S.. Assessing early resistance responses of sugarcane to Xanthomonas albilineans. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 32, n. 10, p. 1-pg., 2019-10-01. (18/07615-4, 16/17545-8)

MIRANDA, RAQUEL P.; TURRINI, PAULA C. G.; BONADIO, DORA T.; ZERILLO, MARCELO M.; BERSELLI, ARTHUR P.; CRESTE, SILVANA; VAN SLUYS, MARIE-ANNE. Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness. MICROBIOLOGY SPECTRUM, v. 11, n. 3, p. 17-pg., 2023-04-13. (08/52074-0, 18/23646-7, 19/05424-0, 18/24646-0, 16/17545-8)

CRESTANA, GUSTAVO SCHIAVONE; TANIGUTI, LUCAS MITSUO; DOS SANTOS, CLESIVAN PEREIRA; BENEVENUTO, JULIANA; CERESINI, PAULO CEZAR; CARVALHO, GISELLE; KITAJIMA, JOAO PAULO; MONTEIRO-VITORELLO, CLAUDIA BARROS. Complete Chromosome-Scale Genome Sequence Resource for Sporisorium panici-leucophaei, the Causal Agent of Sourgrass Smut Disease. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 34, n. 4, p. 448-452, APR 2021. (18/24028-5, 17/13268-2, 16/17545-8)

SOUSA-BAENA, MARIANE S.; HERNANDES-LOPES, JOSE; VAN SLUYS, MARIE-ANNE. Reaching the top through a tortuous path: helical growth in climbing plants. Current Opinion in Plant Biology, v. 59, n. SI, FEB 2021. (16/17545-8, 18/07114-5)

PETERS, L. P.; TEIXEIRA-SILVA, N. S.; BINI, A. P.; SILVA, M. M. L.; MORAES, N.; CRESTANA, G. S.; CRESTE, S.; AZEVEDO, R. A.; CARVALHO, G.; MONTEIRO-VITORELLO, C. B.. Differential responses of genes and enzymes associated with ROS protective responses in the sugarcane smut fungus. FUNGAL BIOLOGY, v. 124, n. 12, p. 1039-1051, DEC 2020. (17/13268-2, 18/07615-4, 16/16376-8, 13/15014-7, 16/17545-8)

FARIA, RAPHAEL S. C. A.; CIA, MARIANA C.; MONTEIRO-VITORELLO, CLAUDIA B.; AZEVEDO, RICARDO A.; CAMARGO, LUIS EDUARDO A.. Characterization of genes responsive to osmotic and oxidative stresses of the sugarcane bacterial pathogen Leifsonia xyli subsp. xyli. Brazilian Journal of Microbiology, v. 51, n. 1, NOV 2019. (15/18681-0, 16/17545-8)

DIAS, HENRIQUE MOURA; VIEIRA, ANDREIA PRATA; DE JESUS, ERIKA MARIA; DE SETTA, NATHALIA; BARROS, GESIELE; VAN SLUYS, MARIE-ANNE. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ, v. 11, p. 27-pg., 2023-05-15. (08/52074-0, 15/05058-2, 16/17545-8, 19/08239-9)

BINI, ANDRESSA PERES; DUARTE SERRA, MARINA CARNAZ; PASTORE, IZADORA FARINA; BRONDI, CAROLINA VELUCI; ARANHA CAMARGO, LUIS EDUARDO; MONTEIRO-VITORELLO, CLAUDIA BARROS; VAN SLUYS, MARIE-ANNE; ROSSI, GUILHERME DUARTE; CRESTE, SILVANA. Transmission of Xanthomonas albilineans by the spittlebug, Mahanarva fimbriolata (Hemiptera: Cercopidae), in Brazil: first report of an insect vector for the causal agent of sugarcane leaf scald. JOURNAL OF INSECT SCIENCE, v. 23, n. 6, p. 8-pg., 2023-11-01. (18/07615-4, 18/21693-8, 16/17545-8)

DIAS, HENRIQUE MOURA; VIEIRA, ANDREIA PRATA; DE JESUS, ERIKA MARIA; DE SETTA, NATHALIA; BARROS, GESIELE; VAN SLUYS, MARIE-ANNE. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ, v. 11, p. 27-pg., 2023-05-15. (16/17545-8, 15/05058-2, 08/52074-0, 19/08239-9)

DIAS, HENRIQUE MOURA; DE TOLEDO, NAIARA ALMEIDA; MURAL, RAVI V.; SCHNABLE, JAMES C.; VAN SLUYS, MARIE-ANNE. THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis. GENOME BIOLOGY AND EVOLUTION, v. 16, n. 10, p. 19-pg., 2024-10-29. (19/08239-9, 22/09923-3, 16/17545-8, 22/16208-9)

BINI, ANDRESSA PERES; ROSSI, GUILHERME DUARTE; POESCHL, YVONNE; SERRA, MARINA CARNAZ DUARTE; CAMARGO, LUIS EDUARDO ARANHA; MONTEIRO-VITORELLO, CLAUDIA BARROS; VAN SLUYS, MARIE-ANNE; DAM, NICOLE M. VAN; UTHE, HENRIETTE; CRESTE, SILVANA. Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease. Plant Physiology and Biochemistry, v. 203, p. 14-pg., 2023-09-25. (18/07615-4, 18/21693-8, 16/17545-8)

SOUSA-BAENA, MARIANE S.; HERNANDES-LOPES, JOSE; VAN SLUYS, MARIE-ANNE. Reaching the top through a tortuous path: helical growth in climbing plants. Current Opinion in Plant Biology, v. 59, p. 8-pg., 2021-02-01. (18/07114-5, 16/17545-8)

RODY, HUGO V. S.; BOMBARDELLI, RENATO G. H.; CRESTE, SILVANA; CAMARGO, LUIS E. A.; VAN SLUYS, MARIE-ANNE; MONTEIRO-VITORELLO, CLAUDIA B.. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. BMC Genomics, v. 20, n. 1, NOV 6 2019. (18/04555-0, 16/17545-8)

MARRAFON-SILVA, MARIANA; MAIA, THIAGO; CALDERAN-RODRIGUES, MARIA JULIANA; STRABELLO, MARIANA; OLIVEIRA, LAINA; CRESTE, SILVANA; MELOTTO, MAELI; MONTEIRO-VITORELLO, CLAUDIA BARROS. Exploring Potential Surrogate Systems for Studying the Early Steps of the Sporisorium scitamineum Pathogenesis. PHYTOPATHOLOGY, v. 114, n. 6, p. 10-pg., 2024-05-24. (16/17545-8, 18/02156-1, 21/02124-5, 19/22911-1, 18/13054-5)