Advanced search
Start date
Betweenand

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

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:
Articles published in other media outlets (0 total):
More itemsLess items
VEICULO: TITULO (DATA)
VEICULO: TITULO (DATA)

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.