Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function

• Grant number: 08/52074-0
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• Start date: May 01, 2009
• End date: January 31, 2015
• 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 ; Joao Paulo Fumio Whitaker Kitajima ; Maria Magdalena Rossi
• Associated scholarship(s): 13/00714-3 - The role of repetitive DNA in the centromeric organization of Saccharum spp, BP.PD; 12/21064-4 - Building a Synthetic Biology Platform for Functional Screening of Promoter Sequences in Plants, BP.PD; 12/02671-7 - At-thi1 homologs in sugarcane: a molecular and functional study, BP.DD; 09/13887-8 - GaTE lab: bioinformatic development in the sugarcane BAC sequencing project, BP.TT

Abstract

Sugarcane is the major feedstock used in Brazil for biofuel production. It corresponds to one of the largest commodities of the agribusiness in the State of Sao Paulo. Bio-ethanol production is dependent on sucrose as the major starting material. Brazilian Sugarcane Industry competitiveness is expected pending the increase in total yield and avoidance of the use of new land for fanning. Increase in biomass production is expected through modulation of sucrose metabolism under beneficial and restrictive growth environments, such as drought. In addition, efficient utilization of bagasse as biomass is mandatory to the whole chain production net yield. This project aims at generating a draft sequence from two specific sugarcane cultivars (R570 and SP80-3280) so that tools are generated for understanding genome polyploidy variation, enable gene discovery and generate a knowledge base molecular infrastructure. Basic research will benefit not only from gene discovery but from the identification of regulatory sequences involved in sucrose metabolism, carbon partitioning in the plant and responses to restrictive water supply. Breeding programs will have access to the development of new molecular markers. Sugarcane corresponds to a highly polyploidy genome among grasses. It is a recent hybrid generated by crosses between Saccharum officinarum and Saccharum spontaneum and its monoploid genome is estimated to be about 1GB comparable in scale to the human and maize genomes. It is proposed to tackle the sugarcane genome by a combined approach of 454 pyrosequencing and Sanger sequencing of 1000 BACs. Available resources are an EST collection generated by SUCEST, array hybridization profiles generated from SUCEST-FUN and a collection R570 BAC clones. BIOEN program will generate a SP80-3280 BAC library which will be screened for homologous R570 BAC sequenced locus to address allelic variation not only in coding regions but also on regulatory sequences. Transposable Elements (TEs) mapping onto these sequenced BACs, array based expression profiles and insertion polymorphism study will provide information concerning their association to genetic diversity in sugarcane crop design The ultimate goal is to contribute with a large scientific community effort to improve sugarcane breeding and develop a systems biology based approach in sugarcane plant biology. (AU)

Scientific publications

(16)

(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)

NAGEL, RAIMUND; TURRINI, PAULA C. G.; NETT, RYAN S.; LEACH, JAN E.; VERDIER, VALERIE; VAN SLUYS, MARIE-ANNE; PETERS, REUBEN J.. An operon for production of bioactive gibberellin A(4) phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola. NEW PHYTOLOGIST, v. 214, n. 3, SI, p. 1260-1266, MAY 2017. (15/24956-1, 12/24954-0, 08/52074-0)

METCALFE, CUSHLA J.; OLIVEIRA, SARAH G.; GAIARSA, JONAS W.; AITKEN, KAREN S.; CARNEIRO, MONALISA S.; ZATTI, FERNANDA; VAN SLUYS, MARIE-ANNE. Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. Journal of Experimental Botany, v. 66, n. 14, SI, p. 4239-4250, JUL 2015. (08/52074-0, 13/09391-2)

MEDEIROS, AMANDA L.; FURTADO, CRISTIANE M.; LEITE, FRANCINALDO S.; SOUTO, VALESKA S.; DE SETTA, NATHALIA; VAN SLUYS, MARIE-ANNE; KITAJIMA, JOAO PAULO; COSTA, ANA PAULA P.; BENEDITO, VAGNER A.; SCORTECCI, KATIA C.. Molecular Genetic Dissection of Sugarcane Flowering under Equatorial Field Conditions. TROPICAL PLANT BIOLOGY, v. 9, n. 4, p. 252-266, DEC 2016. (08/52074-0)

OCHOA CRUZ, EDGAR ANDRES; QUEIROGA CRUZ, GUILHERME MARCELLO; VIEIRA, ANDREIA PRATA; VAN SLUYS, MARIE-ANNE. Virus-like attachment sites as structural landmarks of plants retrotransposons. MOBILE DNA, v. 7, JUL 28 2016. (12/21064-4, 12/02671-7, 08/52074-0)

CRUZ, GUILHERME M. Q.; METCALFE, CUSHLA J.; DE SETTA, NATHALIA; CRUZ, EDGAR A. O.; VIEIRA, ANDREIA PRATA; MEDINA, ROSARIO; VAN SLUYS, MARIE-ANNE. Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons. PLoS One, v. 9, n. 5, MAY 21 2014. (08/52074-0, 12/02671-7)

TANIGUTI, LUCAS M.; SCHAKER, PATRICIA D. C.; BENEVENUTO, JULIANA; PETERS, LEILA P.; CARVALHO, GISELLE; PALHARES, ALESSANDRA; QUECINE, MARIA C.; NUNES, FILIPE R. S.; KMIT, MARIA C. P.; WAI, ALVAN; et al. Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane. PLoS One, v. 10, n. 6, JUN 12 2015. (10/05591-9, 08/52074-0, 12/09524-0, 13/15014-7, 14/21802-0, 13/25599-2)

FIRETTI, FABIANA; ZUNTINI, ALEXANDRE RIZZO; GAIARSA, JONAS WEISMANN; OLIVEIRA, RENATA SOUZA; LOHMANN, LUCIA G.; VAN SLUYS, MARIE-ANNE. Complete chloroplast genome sequences contribute to plant species delimitation: A case study of the Anemopaegma species complex. AMERICAN JOURNAL OF BOTANY, v. 104, n. 10, p. 1493-1509, OCT 2017. (08/52074-0, 11/50859-2, 12/50260-6, 13/10362-7)

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)

METCALFE, CUSHLA J.; OLIVEIRA, SARAH G.; GAIARSA, JONAS W.; AITKEN, KAREN S.; CARNEIRO, MONALISA S.; ZATTI, FERNANDA; VAN SLUYS, MARIE-ANNE. Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. Journal of Experimental Botany, v. 66, n. 14, p. 12-pg., 2015-07-01. (08/52074-0, 13/09391-2)

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)

BARROS-CARVALHO, GESIELE ALMEIDA; HUNGRIA, MARIANGELA; LOPES, FABRICIO MARTINS; VAN SLUYS, MARIE-ANNE. Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation. FEMS Microbiology Letters, v. 366, n. 11, JUN 2019. (08/52074-0)

DE SETTA, NATHALIA; MONTEIRO-VITORELLO, CLAUDIA BARROS; METCALFE, CUSHLA JANE; QUEIROGA CRUZ, GUILHERME MARCELO; DEL BEM, LUIZ EDUARDO; VICENTINI, RENATO; SILVEIRA NOGUEIRA, FABIO TEBALDI; CAMPOS, ROBERTA ALVARES; NUNES, SIDENY LIMA; GASPERAZZO TURRINI, PAULA CRISTINA; et al. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, v. 15, JUN 30 2014. (10/05591-9, 08/54201-9, 08/52074-0, 08/58031-0, 08/52197-4, 08/52146-0)

DOMINGUES, DOUGLAS S.; CRUZ, GUILHERME M. Q.; METCALFE, CUSHLA J.; NOGUEIRA, FABIO T. S.; VICENTINI, RENATO; ALVES, CRISTIANE DE S.; VAN SLUYS, MARIE-ANNE. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics, v. 13, APR 16 2012. (08/52074-0)

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)

NAGEL, RAIMUND; TURRINI, PAULA C. G.; NETT, RYAN S.; LEACH, JAN E.; VERDIER, VALERIE; VAN SLUYS, MARIE-ANNE; PETERS, REUBEN J.. An operon for production of bioactive gibberellin A(4) phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola. NEW PHYTOLOGIST, v. 214, n. 3, p. 7-pg., 2017-05-01. (08/52074-0, 12/24954-0, 15/24956-1)

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, 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)