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

Grant number: 12/51062-3
Support type: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
Cooperation agreement: Microsoft Research
Principal Investigator:Glaucia Mendes Souza
Grantee:Glaucia Mendes Souza
Home Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Company: Microsoft
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)

Articles published in Agência FAPESP Newsletter about the research grant
Most complete commercial sugarcane genome sequence has been assembled 
Articles published in other media outlets (55 total):
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Concluyen la mayor secuenciación del genoma de la caña de azúcar comercial 
Publican la secuencia genómica más completa de la caña de azúcar comercial 
Publican la secuencia genómica más completa de la caña de azúcar comercial 
Científicos brasileños publican la secuencia genómica más completa de caña de azúcar comercial 
Científicos brasileños publican la secuencia genómica más completa de caña de azúcar comercial 
Cientistas brasileiras lideram o maior e mais completo mapeamento genético já feito da cana-de-açúcar 
Cientistas brasileiras quebram um recorde da genética 
Concluyen la mayor secuenciación del genoma de la caña de azúcar comercial 
Científicos brasileños publican la secuencia genómica más completa de la caña de azúcar comercial 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Montada sequência de genoma mais completo da cana 
Most complete commercial sugarcane genome sequence assembled 
Cientistas brasileiras lideram mapeamento genético da cana-de-açúcar 
Montada sequência de genoma mais completo da cana 
Montada sequência de genoma mais completo da cana 
Cientistas do Brasil decifram genoma da cana-de-açúcar 
Brazilian scientists sequence “most complete” commercial sugarcane genome 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Concluído maior sequenciamento do genoma da Cana-de-Açúcar comercial 
Duas cientistas brasileiras lideram o maior e mais completo mapeamento genético já feito da cana-de-açúcar 
Montada sequência de genoma mais completo da cana 
Cientistas quebram um recorde da genética com o sequenciamento do genoma da cana-de-açúcar 
Brazilian Scientists Publish Most Complete Genome Sequence of Commercial Sugarcane 
Cientistas brasileiras quebraram um recorde de genética 
Pesquisadores desvendam genoma da cana de açúcar 
MAIS SEQUCIA COMERCIAL ABRANGENTE DO GENOMA DE CANA MONTADO 
Grupo da USP publica o mais completo genoma da cana 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Grupo da USP publica o mais completo genoma da cana-de-açúcar 
Grupo da USP publica o mais completo genoma da cana 
Concluído maior sequenciamento do genoma da Cana de Açúcar comercial 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Concluído maior sequenciamento do genoma da Cana de Açúcar comercial 
Cientistas brasileiras quebram um recorde da genética 
Most complete commercial sugarcane genome sequence assembled 
Cientistas brasileiras quebram um recorde da genética 
Concluído maior sequenciamento do genoma da cana-de-açúcar comercial 
Cientistas brasileiros lideram mais completo mapeamento do genoma da cana 
Grupo da USP publica o mais completo genoma da cana de açúcar 
Concluído maior sequenciamento do genoma da Cana de Açúcar comercial 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Concluído maior sequenciamento do genoma da Cana de Açúcar comercial 
Cientistas brasileiras quebram um recorde da genética 
Most complete commercial sugarcane genome sequence has been assembled 
Concluído maior sequenciamento do genoma da cana-de-açúcar comercial 
Cientistas brasileiros lideram mais completo mapeamento do genoma da cana 
Cientistas brasileiros lideram mais completo mapeamento do genoma da cana 
Most complete commercial sugarcane genome sequence has been assembled 
Concluído o maior sequenciamento do genoma da cana-de-açúcar comercial 
Most Complete Commercial Sugarcane Genome Sequence Has Been Assembled 
Most complete commercial sugarcane genome sequence has been assembled 
Most complete commercial sugarcane genome sequence has been assembled 
Most complete commercial sugarcane genome sequence has been assembled 
Pesquisadores encontram mais de 370 mil genes em cultivar comercial da cana-de-açúcar 

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; NISHIYAMA, MILTON YUTAKA; TEN-CATEN, FELIPE; RAGAGNIN, GEOVANI TOLFO; ANDRADE, PABLO DE MORAIS; DE SOUZA, ROBSON FRANCISCO; NICASTRO, GIANLUCCA GONCALVES; PANDYA, RAVI; KIM, CHANGSOO; GUO, HUI; DURHAM, ALAN MITCHELL; CARNEIRO, MONALISA SAMPAIO; ZHANG, JISEN; ZHANG, XINGTAN; ZHANG, QING; MING, RAY; SCHATZ, MICHAEL C.; DAVIDSON, BOB; PATERSON, ANDREW H.; HECKERMAN, DAVID. 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. Web of Science Citations: 3.
ZHANG, JISEN; ZHANG, XINGTAN; TANG, HAIBAO; ZHANG, QING; HUA, XIUTING; MA, XIAOKAI; ZHU, FAN; JONES, TYLER; ZHU, XINGUANG; BOWERS, JOHN; WAI, CHING MAN; ZHENG, CHUNFANG; SHIL, YAN; CHEN, SHUAI; XU, XIUMING; YUE, JINGJING; NELSONS, DAVID R.; HUANG, LIXIAN; LI, ZHEN; XU, HUIMIN; ZHOU, DONG; WANG, YONGJUN; HU, WEICHANG; LIN, JISHAN; DENG, YOUJIN; PANDEY, NEHA; MANCINI, MELINA; ZERPA, DESSIREE; NGUYEN, JULIE K.; WANG, LIMING; YU, LIANG; XIN, YINGHUI; GE, LIANGFA; ARRO, JIE; HAN, JENNIFER O.; CHAKRABARTY, SETU; PUSHKO, MARIJA; ZHANG, WENPING; MA, YANHONG; MA, PANPAN; LV, MINGJU; CHEN, FAMING; ZHENG, GUANGYONG; XU, JINGSHENG; YANG, ZHENHUI; DENG, FANG; CHEN, XUEQUN; LIAO, ZHENYANG; ZHANG, XUNXIAO; LIN, ZHICONG; LIN, HAI; YAN, HANSONG; KUANG, ZHENG; ZHONG, WEIMIN; LIANG, PINGPING; WANG, GUOFENG; YUAN, YUAN; SHI, JIAXIAN; HOU, JINXIANG; LIN, JINGXIAN; JIN, JINGJING; CAO, PEIJIAN; SHEN, QIAOCHU; JIANG, QING; ZHOU, PING; MA, YAYING; ZHANG, XIAODAN; XU, RONGRONG; LIU, JUAN; ZHOU, YONGMEI; JIA, HAIFENG; MA, QING; QI, RUI; ZHANG, ZHILIANG; FANG, JINGPING; FANG, HONGKUN; SONG, JINJIN; WANG, MENGJUAN; DONG, GUANGRUI; WANG, GANG; CHEN, ZHENG; MA, TENG; LIU, HONG; DHUNGANA, SINGHA R.; HUSS, SARAH E.; YANG, XIPING; SHARMA, ANUPMA; TRUJILLO, JHON H.; MARTINEZ, MARIA C.; HUDSON, MATTHEW; RIASCOS, JOHN J.; SCHULER, MARY; CHEN, LI-QING; BRAUN, DAVID M.; LI, LEI; YU, QINGYI; WANG, JIANPING; WANG, KAI; SCHATZ, MICHAEL C.; HECKERMAN, DAVID; VAN SLUYS, MARIE-ANNE; SOUZA, GLAUCIA MENDES; MOORE, PAUL H.; SANKOFF, DAVID; VANBUREN, ROBERT; PATERSON, ANDREW H.; NAGAI, CHIFUMI; MING, RAY. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.. Nature Genetics, v. 50, n. 11, p. 1565+, NOV 2018. Web of Science Citations: 37.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.