Development of an algorithm for the assembly of the sugarcane polyploid genome

• Grant number: 12/51062-3
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Research Partnership for Technological Innovation (PITE)
• Duration: February 01, 2013 - January 31, 2016
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Convênio/Acordo: Microsoft Research
• Principal Investigator: Glaucia Mendes Souza
• Grantee: Glaucia Mendes Souza
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• City: São Paulo
• Partner institutions: Microsoft
• Associated grant(s): 15/50102-0 - Extending synthetic biology collaborations between WISB and BSSB, AP.R SPRINT
• Associated scholarship(s): 13/21503-0 - Development of an algorithm for the assembly of the sugarcane polyploid genome, BP.TT

Abstract

The challenges in sequencing the sugarcane genome relies in the assembly and to analyze a highly complex genome that is polyploid and aneuploid, with a complete set of homologous genes predicted to range from 10 to 12 copies (alleles). The present project aim to improve, through the development of new algorithms, the assembly from shotgun reads of datasets generated by the BIOEN research groups. We intend to combine shot-gun sequencing data obtained using 454 and Illumina using different protocols to assemble a reference genome for cultivar SP80-3280. To accomplish assembly the group will develop algorithms to enable the recognition of multiple copies of any given region of the reference genome. The group will perform comparative analysis with other genomes, especially sorghum that is very synthenic to sugarcane, to evaluate the quality of the assembled sequence. Existing data on the sugarcane transcriptome will be integrated to validate gene models and infer gene function. Microsoft will develop algorithms for assembly of the sugarcane polyploid genome to strengthen allele Identification and improve assembly. The results will contribute to the advancement of knowledge in plant genomics, establishment of computational infrastructure and the formation of highly qualified human resources in bioinformatics. In the long term, we expect to create computational biology tools to resolve polyploid genomes first with the sugarcane genomics but that may also be applied to other cultivated polyploid crops. (AU)

Scientific publications

(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)

ZHANG, JISEN; ZHANG, XINGTAN; TANG, HAIBAO; ZHANG, QING; HUA, XIUTING; MA, XIAOKAI; ZHU, FAN; JONES, TYLER; ZHU, XINGUANG; BOWERS, JOHN; et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.. Nature Genetics, v. 50, n. 11, p. 1565+, NOV 2018. (14/50921-8, 12/51062-3, 08/52146-0)