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

Grant number: 08/52074-0
Support type:Program for Research on Bioenergy (BIOEN) - Thematic Grants
Duration: May 01, 2009 - January 31, 2015
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:Marie-Anne Van Sluys
Grantee:
Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo, SP, Brazil
Co-Principal Investigators: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)

Articles published in Agência FAPESP about the research grant
Study clarifies process of sugarcane genome evolution 
Ethanol takes off 
Articles published in Revista Pesquisa FAPESP about the project
Wandering DNA  

Scientific publications (8)
(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. Web of Science Citations: 1.
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. Web of Science Citations: 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. Web of Science Citations: 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. Web of Science Citations: 3.
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; HAUSNER, GEORG; AITKEN, KAREN S.; BERKMAN, PAUL J.; FRASER, JAMES A.; MOOLHUIJZEN, PAULA M.; COUTINHO, LUIZ L.; CRESTE, SILVANA; VIEIRA, MARIA L. C.; KITAJIMA, JOAO P.; MONTEIRO-VITORELLO, CLAUDIA B. Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane. PLoS One, v. 10, n. 6 JUN 12 2015. Web of Science Citations: 19.
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; VIEIRA, ANDREIA PRATA; OCHOA CRUZ, EDGAR ANDRES; SILVEIRA CORREA, TATIANA CAROLINE; HOTTA, CARLOS TAKESHI; VARANI, ALESSANDRO DE MELLO; VAUTRIN, SONIA; DA TRINDADE, ADILSON SILVA; VILELA, MARIANE DE MENDONCA; LEMBKE, CAROLINA GIMILIANI; SATO, PALOMA MIEKO; DE ANDRADE, RODRIGO FANDINO; NISHIYAMA, JR., MILTON YUTAKA; CARDOSO-SILVA, CLAUDIO BENICIO; SCORTECCI, KATIA CASTANHO; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO, MONALISA SAMPAIO; KIM, CHANGSOO; PATERSON, ANDREW H.; BERGES, HELENE; D'HONT, ANGELIQUE; DE SOUZA, ANETE PEREIRA; SOUZA, GLAUCIA MENDES; VINCENTZ, MICHEL; KITAJIMA, JOAO PAULO; VAN SLUYS, MARIE-ANNE. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, v. 15, JUN 30 2014. Web of Science Citations: 21.
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. Web of Science Citations: 1.
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. Web of Science Citations: 23.

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