News
Genome kickoff
July 30, 2009
FAPESP News – The decoding of the genome of the sugarcane plant is underway in Brazil. At the University of São Paulo, a group of scientists funded by FAPESP’s Program for Research on Bioenergy (BIOEN) recently obtained the first 1.1 million reads using a pyrosequencer, a cutting-edge machine for genetic analysis.
The next test of the machine will begin next week. Due to the large amount and high complexity of the data generated by the new approach, the BIOEN Program is expanding its bioinformatics team and is now looking to hire database researchers, software developers and statisticians.
Agreementing to the director of the BIOEN Program, Glaucia Mendes de Souza, a professor at the USP Institute of Chemistry, the first batch of DNA sequenced with the new machine has already generated more than 11 times as much data as that generated during the first two years of the Sugarcane Expressed Sequence Tag (SUCEST) Project, also known as the Cane Genome Project.
The pyrosequencer is located at the Centro Avançado de Tecnologias em Genômica (CATG, Advanced Genome Technology Center). “In just one run we generated nearly 335 million base pairs. By comparison, the sequencing done by SUCEST between 2001 and 2003 generated slightly fewer than 30 million base pairs,” she said in an interview with FAPESP News.
The experiment was carried out at CATG by Carlos Hotta, the recipient of a post-doctoral research grant from FAPESP. The work is part of “Regulatory and Signal Networks of Sugarcane,” a thematic project supported by FAPESP and led by Souza.
“CATG, opened in 2008, is led by Professor Sergio Verjovski-Almeida [of the USP Institute of Chemistry]. The Roche 454 pyrosequencer used in this experiment was purchased for $500,000 using funds from the Financing Agency for Studies and Projects. FAPESP financed the purchase of the sequencing reagents needed for 100 runs with another $1 million. The additional projects costs will add another $4 million beyond that,” explained Souza.
Agreementing to Souza, the goal of the experiment is to identify promoter regions and variants that control gene expression, as well as to catalog genetic diversity, in order to assist efforts to improve sugarcane varieties.
“The 454 pyrosequencer is the best approach to sequencing sugarcane because it allows researchers to study relatively large DNA fragments of 450 base pairs. That’s helpful because sugarcane has a large genome, with more than 10 billion base pairs, and many sections that are repeats,” she explained.
The technique used with a pyrosequencer, known as shotgun sequencing, was also used in the decoding of the human genome. Instead of being copied, or cloned, the genome is instead “shredded” into small fragments which are then sequenced on a large scale. “But the human genome took more than ten years to sequence, because the 454 was not available at the time,” she noted.
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The SUCEST Project—which involved 240 researchers from more than 40 institutions, including 17 institutions outside of Brazil—evaluated the transcriptome of sugarcane and developed a huge database on the plant’s genes. That was done by sequencing gene fragments known as expressed sequence tags.
“That project gave us a starting point for the creation of the BIOEN Program. For the next step, we decided it was important to move beyond expressed sequences to complete sequences, because that allows us to reconstruct regulatory networks, among other things,” said Souza.
“For example, if we want to know how sugarcane builds up sucrose and why one plant makes a lot of it and another less, we need to understand the metabolic networks involved in sucrose synthesis. To know how the plant turns those networks on and off, we need to identify the genes and their regulatory regions, called promoters,” she explained.
The promoters, she said, indicate where, when and how much a specific gene is being expressed. “What regulates the physiology of a plant—responses to stress, sugar metabolism and growth, for example—are these groups of genes that influence the metabolic networks,” she said.
Agreementing to Souza, the BIOEN Program plans to invest enough resources for about 100 runs with the 454 machine. “That will allow us at least 5× coverage of the sugarcane genome,” she stated.
Nevertheless, the researchers involved in the BIOEN Program plan to sequence in additional detail about 1,000 longer pieces of the sugarcane genome that are of specific interest to the program, including genes associated with high sucrose production and resistance to drought.
“About 300 pieces will come from the variety known as R570 – used globally as a model for genetic improvement of cane – and another 700 will come from Brazilian varieties. But it’s important to note that we are not going to finish the cane genome until the conclusion of these thematic projects,” she said.
With the help of the pyrosequencer, the researchers plan to obtain a draft of the sugarcane genome within five years, and subsequently sequence in detail large fragments of over 100,000 base pairs inserted into bacterial artificial chromosomes.
Souza says the work is part of an international strategy involving Brazil, Australia, South Africa, France and the United States. “Each member of the consortium will make a draft genome sequence of varieties of interest and we’ll work together to try to integrate the data into a global genomic database for sugarcane,” she said.
To achieve that goal, an international bioinformatics team is being established. “In Brazil, we’re looking for people to analyze the data, and we need talent in areas like mathematics, statistics, computer science and systems engineering. The development of the database is going to require a lot of work,” she said.
Agreementing to Souza, having the sequencing technology up and running, having a team in place, constructing a database and exchanging information with international research groups are all essential to taking our understanding of sugarcane to the next level.
“Sugarcane today is where corn was ten years ago, and that’s why we don’t have the biotechnology tools we need to improve it. It’s really hard to understand how cane varieties have been improved, because there isn’t any statistical genetics software to analyze a genome as complex as this one,” she said.
BIOEN Program site: http://bioenfapesp.org
Media Contacts
Fernando Cunha, FAPESP (www.fapesp.br) / (+55) 11 3838-4151
São Paulo Research Foundation – FAPESP – is an independent public foundation with the mission to foster research and the scientific and technological development of the State of São Paulo, Brazil. This is achieved through the support of research projects carried out in higher education and research institutions, in all fields of knowledge.