The Onsa Network

The São Paulo Virtual Genomics

InstituteThese transparencies should be viewed as a complementary material to the paper “ONSA, The São Paulo Virtual Genomics Institute” Nature

Biotechonology Vol.16, 795-796, 1998

Fapesp´s Genome: Fapesp´s Genome: from project to program - a Chronologyfrom project to program - a Chronology• MOTIVATION: BIOTECHONOLOGY• May 01.97 INITIAL IDEA• MEETINGS WITH SCIENTISTS• INTERNATIONAL CONSULTANTS

(A. Goffeau 06.13, S.Oliver)• INDUSTRIAL PARTNERS• CHOICE OF ORGANISM• 10.13.97 CALL FOR APPLICATIONS• 11.15.97 DEADLINE FOR APPLICATIONS• 11.16.97 SELECTION OF LABS

ONSA ONSA The Original The Original ArchitectureArchitecture

• DNA COORDINATOR

Andrew Simpson (Ludwig ICR - SP)

• TWO CENTRAL LABS

USP (Reinach) - UNICAMP (Arruda)

• 32 SEQUENCING LABS

• BIOINFORMATICS CENTER

UNICAMP (Setubal & Meidanis)

• 11.17.97 PURCHASE OF EQUIPMENT• Dec.97 COPERSUCAR and Sugarcane• Jan. 98 CGAP and the Cancer Project• 05.01.98 START SEQUENCING• 07.98 APPROVAL OF A GENOME PROGRAM

FUNCTIONAL GENOMICS: “UNDERSTANDING CVC FROM Xf´S GENOME” : CALL FOR PROPOSALS

• 01/99 FUNCTIONAL GENOMICS - 21 PROJECTS

ChronologyChronology

• 02.99 GENE PATENT SUBMISSION• 03.99 BEGIN OF FUNCTIONAL GENOMICS

Number of participating labs: 21• GENOME CONCLUSION:

INITIAL GOAL: JUNE 2000

ACTUAL CONCLUSION: JANUARY 2000• NATURE VOL.406 JULY 13

Estimated genome size 2.1 Mb

Genome size: revised 2.7 Mb

Sugarcane EST Project SUCEST

• Goal: sequence circa 50 000 genes of Sugarcane by April 2001

• DNA coordinator: Paulo Arruda (Unicamp)• Bioinformatics UNICAMP• 03.99 Call for application • 04.99 Choice of participant labs

HUMAN CANCER GENOME PROJECT

• PARTNERSHIP LICR - FAPESP

• NOVEL METHODOLOGY:

ORESTES (OPEN READING FRAMES ESTs)

DNA COORDINATOR - SIMPSON

• Tumors: Colon, Stomach, Head, Neck, Cervix

• Call for applications: April 99

• Choice of labs: June 99

• Initial Goal: 500.000 SEQUENCES - June 2001

• Revised Goal: 1.000.000 SEQUENCES - September 2000

BUDGETBUDGET

• Xylella fastidiosa: US$ 13 mi• Functional Genomics: US$ 4 mi• CANCER: US$ 10mi (1999) + 10 mi (2000)

LICR + FAPESP

• SUGARCANE: US$ 6 MILLION

• Xanthomonas axonopodis citri: US$ 5 MILLION

The Enlarged ONSA The Enlarged ONSA

65 labs through out the State of São Paulo

300 researchers

ONGOING PROJECTS

• XANTHOMONAS CITRI (4.7 Mb)

Expected Conclusion December 2000

• GRAPEVINE´S Xf (USDA + AVF)

• CLAVIBACTER XYLI (SUGARCANE CONSORTIUM)

MEDIA VISIBILITYMEDIA VISIBILITY

• NATURE

• NEWSPAPERS

• MAGAZINES

• RADIO

• TV SERIES - 5 PROGRAMS

(SÃO PAULO) Brazilian researchers have entered the competitive field of human genome sequencing with the signing of an agreement between the state funding agency of São Paulo (FAPESP) and US-based Ludwig Institute for Cancer Research.

Each will contribute US$ 5 million to two-year Human Cancer Genome Project. According to FAPESP, the programme is "aimed at providing sequences from genes expressed in tumours that are important within the context of public health in the state of São Paulo".

The project will sequence and analyse short DNA fragments created from the central coding portions of human genes. Although a US patent is being sought for the technique used to generate these expressed sequence tags (ESTs), the sequences will be freely available on the Internet. "No sequences will be patented. All the data will be promptly published", says Ed McDermott Jr., president of the Ludwig Institute, who visited Brazil to sign the agreement.

The programme follows on from the Organization for Nucleotide Sequencing and Analysis (ONSA), a network of 30 laboratories in the state of São Paulo now in the final steps of sequencing the complete genome of the plant pathogen Xylella fastidiosa. The groups will build upon their experience with this pathogen, which causes many

economically important plant diseases, notably citrus variegated chlorosis, which poses a major threat to São Paulo's orange farming (see Nature 389, 654; 1997).

ONSA is a "virtual" institute that links the sequencing laboratories, keeping down costs and red tape. The acronym, which sounds like the word onça (jaguar) in Portuguese, mimics the Institute for Genomic Research (TIGR), according to José Fernando Perez, FAPESP's scientific director.

Five centres will carry out the sequencing, each helped by four other labs. The centres will be at the chemistry institute, the faculty of medicine at São Paulo, and the faculty of medicine at Ribeirão Preto, all from the University of São Paulo; at the Paulista School of Medicine, São Paulo; and at the Hemocentro of the University of Campinas. The programme aims to generate between 500,000 and 750,000 EST sequences, and about 200 million bases of human genome sequence.

The project will be monitored by a four-member steering committee, composed of Marcelo Bento Soares of the University of Iowa, John Sgouros of the Imperial Cancer Research Fund in Londo, and Webster Cavenee and Richard Kolodner of the Ludwig Institute in San Diego.

Ricardo Bonalume Neto

Brazilian scientists team up for cancer genome project.

São Paulo. The creation of a network of laboratories in São Paulo state, Brazil, to sequence the complete genome of a microorganism was announced last week by the Foundation for the Support of Research of the State of São Paulo (FAPESP),

The Organisation for Nucleotide Sequencing and Analysis will first tackle the bacterium Xylella fastidiosa, the causal agent of many economically important plant diseases, particularly citrus variegated chlorosis, which poses a major threat to São Paulo's orange cultivation. This is thought to be the first plant pathogen genome to have been sequenced.

Citrus variegated chlorosis, first reported in 1987, has been found only in Brazil and Argentina. São Paulo and Florida are the two most important citrus-growing areas in the world, São Paulo producing 87 per cent of Brazil's -- and 30 per cent of the world's -- citrus crop. According to FAPESP, the total cost of the project is US$11.6 million, to be spent over two years. Sequencing completion is predicted by 2000.

Xylella fastidiosa was chosen because sequencing might help in the control of the pest, with obvious gains to the state's economy. It will also help to forge links between research centres and the private sector, which is contributing to the cost of the project.

The state says that it is keen to create a network of laboratories that will "significantly increase the number of laboratories in the state capable of using modern molecular biology techniques".

The project will be overseen by a five-member steering committee onsisting of three international experts in genome sequencing and two researchers from São Paulo state. Two of the experts, André Goffeau of the University of Louvain in Belgium and Steve Oliver of the University of Manchester Institute of Science and Technology, helped to set up the project, and were also involved in the sequencing of the Saccharomyces cerevisiae genome.

The committee will select one laboratory to house a bioinformatics centre. Two large central sequencing laboratories will be chosen to generate a large part of the sequence data. These laboratories will also act as training and support centres for

other members of the network.

Ricardo Bonalume Neto

Brazil to sequence ´first plant pathogen´

A Genome Cinderella Story

In 1987 orange growers in the Brazilian state of São Paulo first noticed the telltale signs of a new disease: conspicuous yellow patches on individual leaves. The fruits on these spotted trees turned out to be small, hard, and gave little juice, rendering them commercially useless. Today, citrus variegated chlorosis (CVC)--as the disease is known--threatens the entire citrus industry in São Paulo state, the world's largest exporter of concentrated orange juice. The disease affects more than 30% of all trees and causes losses estimated at $100 million each year.

Now scientists have a new tool to attack this devastating microbe. On 12 April a team reported at the meeting that they had deciphered the 2.7-million-base-pair genome of Xylella fastidiosa, the causative agent. X. fastidiosa is the first bacterial plant pathogen ever to be fully sequenced. What's more, the feat was pulled off not by one of the sequencing superstars in the United States or Europe but by a consortium of some 30 labs in São Paulo state--groups with little or no previous genomic expertise.

This coup earned the Brazilian scientists ample praise from their international peers. Raves biochemist André Goffeau of the École Normale Superieure in Paris: "The quality [of the sequence] is superb. It's incredible how fast they've done it, given that 2 years ago they didn't even have the [sequencing] machines." The X. fastidiosa genome "is quite a big deal," says Edwin Civerolo, a plant pathologist with the U.S. Department of Agriculture (USDA) who works at the University of California, Davis. Indeed, the work is so impressive that the USDA and the state of California have just enlisted--to the tune of $250,000--the Brazilian team to sequence a related strain of X. fastidiosa that causes Pierce's disease and is threatening vineyards across California.

The X. fastidiosa genome project was conceived in 1997 when Fernando Perez, scientific director of the State of São Paulo Research Foundation (FAPESP), a state-run public funding agency, became concerned about the lack of genomics research in Brazil. After consulting some of Brazil's top life scientists, Perez and his scientific advisers decided that Brazil should embark on its own genome project. But what to sequence?

GENOMES 2000:

Intimate Portraits of Bacterial Nemeses

Michael Hagmann

Historical perspectiveHigh-throughput sequencing is a highly specialised trade, practised

in a very limited number of laboratories in the developed world. It can be estimated that a dozen labs are contributing over half the total sequence data currently being deposited in the public databases, with another 50 or so accounting for the bulk of the rest. All of these labs are located in North America, the larger European countries, Australia and Japan. It may thus come as a surprise that the latest entrant in this select club hails from Brazil, and more specifically the state of São Paulo.

São Paulo has a law stating that 1% of the tax revenue collected by the state has to be given to an independent agency that supports scientific research, known as FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo). As São Paulo is the richest state in Brazil, this amounts to a considerable amount of money (USD 250 Mio in 1998). By law, FAPESP is also forbidden to spend more than 5% of its money on administrative costs. The combination of ample funding and political independence gives the Foundation a lot of freedom to develop innovative scientific programs.

In 1997, FAPESP decided that Brazil should not miss out on the scientific and economic opportunities that can be derived from genome sequencing, and should be able to produce its own data, analyse them, and use the results for local scientific projects. To start off, it was decided that a good target rganism should be bacterial, and of interest to the local economy.

The agency settled on Xylella fastidiosa, a bacterium that infects orange trees, a major source of income in São Paulo, and causes Citrus Variegated Chlorosis. This choice also brought in additional funding from the citrus growers' association (Fundecitrus).

ONSA

A major goal of this first genome project was to bring sequencing technology to as many laboratories as possible, thus propelling them into the genome age. Therefore, the concept of setting up a single sequencing centre was rejected from the start. Instead, bids were put up for laboratories interested in participating in the project, and those that were selected received equipment (ABI370 sequencers), reagents, and ample technical advice. In total, 30 labs were selected for the Xylella project, dispersed geographically throughout the state of São Paulo. In addition to the sequencing labs, the project steering committee designated a DNA co-ordinator (for the handling and distribution of clones) and a bioinformatics centre. The bioinformatics group, located at the University of Campinas (about 80 km from São Paulo), was made responsible for all of the data handling, from base calling to final assembly verification. The sequencing labs submitted trace files only, and were paid on the basis of the amount of non-vector, high-quality sequences (based on phred scores) that could be extracted from their data. The entire process was automated using Web pages, and enabled the bioinformatics group to keep very close tabs on the daily progress of the project as a whole.

Brazil, a new Mecca for genomics?

EUROPEAN MOLECULAR BIOLOGY NETWORK - EMBNET

Los Angeles Times By Melinda Fulmer

April, 15, 2000

Cinderella GenesCinderella Genes

Brazil was the poor sister of genome research, until its scientists pulled of two world-class coups

By Mac Margolis NEWSWEEK INTERNATIONAL

August 6 - Brazilian biochemist Sandro de Souza, 32, ha landed a dream job at Harvard University. His boss was physicist and Nobel laureate Walter Gilbert, practically a deity in the world of DNA sequencing. Then the phone rang. A friend asked Souza to join a new genome research project - in Brazil, of all places. To his surprise, Souza took a deep breath and accepted. "I wondered what would become of me," he recalls.

THAT WAS TWO whole years ago, before Brazil, a backwater of genetic research, metamorphosed into an international powerhouse. Last month researchers at Sao Paulo's fapesp research institute announced that they had cracked the DNA code of Xylella fastidiosa, a bacterial pest that destroys a third of Brazil's orange crop each year. It is the first time scientists had ever mapped the structure of the genome of a plant pathogen - a "landmark achievement," as the British journal Nature put it.

As if that weren't enough, a week later Souza's own group announced that it had successfully mapped the structure of some 500,000 human expressed-sequence tags (EST) in malignant tumors. ESTs are tiny bits of DNA that scientists use to piece together the far longer sequence of base pairs that make up a gene. The more ESTs you know for a particular tumor, the better your chance of being able

to decode the entire structure of its genome and eventually to find a cure. Only the United States and Britain haveidentified more human ESTS. Ali of a sudden, Souza and his fellow Brazilians are sitting pretty at the top of an important field of research. "This is the leading edge," said Richard Klausner, president of the National Cancer Institute, who works closely with the Brazilians. "TheBrazilian team has shown that emerging nations can participate as equals in cutting-edge research.”

How did Brazil pull off such a feat? Slowly at first, then all at once. The slow part was Fapesp's rise to the research big leagues. Fapesp takes a 1 percent share of Sao Paulo'sstate tax revenues, which has allowed the 50-year-old institute to nourish a fat endowment and fund quality research into everything from airplane dynamics to weather prediction.

"The Brazilian team has shown that engineering nations can particpate as equals in cutting- edge research."RICHARD KLAUSNER president of the National Cancer Institute

SAMBA, football and...genomics. The list of things for which Brazil is renowned has suddenly got longer. Only a few days after publishing, on July 13th, the first-ever sequence of the genome of a plant pathogen, scientists at Sao Paulo’s state research agency, Fapesp, were due to announce, on July 21st, another success—the composition of 279,000 human expressed-sequence tags, small pieces of DNA that allow genes to be located along chromosomes. Only in America and Britain have more than that number of human ESTs been identified.

Though they are of global significance, both of these advances are also of particular interest to Brazilians. A number of the ESTs in question are derived from genes linked to cancer of the head and neck, which for some reason is unusually common in Brazil. And the plant pathogen sequenced, Xylella fastidiosa, is an insect-borne bacterium that has been ravaging Brazil’s orange groves, causing their trees to produce shrivelled fruit and costing growers an estimated $100m a year.

As if sequencing X. fastidiosa were not enough of an achievement in itself, the project was finished two months ahead of schedule and $2m under its original $15m budget, even though it involved co-ordinating a "virtual institute" made up of 35 laboratories scattered across the state. The man who did that co-ordinating, Andrew Simpson, says there were two reasons for arranging things this way. The alternative, building a giant, bricks-and-mortar institute would have been costly and time-consuming. And dividing the work between many laboratories maximised the sharing of know-how among Sao Paulo’s scientists.

Brazilian scienceFruits of co-operation

Peter Collins S A O P A U L O

The EconomistJuly 22nd-29th, 2000 - Ed. no. 8180

This sudden leap in scientific expertise has had a long run-up. Ever since the 1960s, Fapesp has been guaranteed, by law, a fixed share of all the tax collected in Sao Paulo (first 0.5%, later 1%) and independence from the political meddling that is endemic in Brazilian public institutions. And whereas other states’ research agencies have such guarantees routinely ignored, Fapesp’s growing prestige over the years has made it increasingly hard for local politicians to interfere or pinch its money. By late 1997 it was possible for the agency to decide that, although there had until then been only some limited sequencing of individual genes, the state’s laboratories were ready to jump into a huge project and sequence a complete organism.

The success of the X. fastidiosa project seems to be breeding more success—and more money. The Brazilian citrus growers’ association, which helped to finance the project, is now offering to pay to decode the bug that causes another serious disease, citrus canker. The Ludwig Institute, in Switzerland, is contributing half of the $10m cost of the team’s human-cancer project. Brazilian sugar growers are helping to finance another new project, to sequence the genome of sugarcane. And the American Department of Agriculture is to pay for a team to sequence a strain of X. fastidiosa that causes Pierce’s disease in grapevines, which is currently afflicting California’s vineyards.

The lesson of all this is that there is no reason why countries such as Brazil cannot compete in leading-edge science if they put their minds to it. Brazil’s share of the scientific papers published in international journals has risen from 0.4% to 1.2% over the past 15 years. With its largest state having now demonstrated the benefits of co-operation and a secure source of financing, and with more than 200 young geneticists trained as a result of the X. fastidiosa project alone, that share may well go on rising.

The EconomistJuly 22nd-29th, 2000 - Ed. no. 8180

July 18, 2000

Agriculture Takes Its Turn in the Genome SpotlightBy CAROL KAESUK YOON

Xylella fastidiosa Genome Project An electron micrograph of the

bacterium Xylella fastidiosa.

In a scientific first, and a coup for science in Brazil, a team of more than 200 researchers there has for the first time deciphered the complete DNA sequence of an organism that causes a plant disease.

Though other genome sequencing efforts -- for example, in humans or the laboratory staple fruit fly -- have attracted more attention, the Brazilian target, an odd little bacterium known as Xylella fastidiosa, distinguishes itself as the first to be decoded of the countless nasty species that together cost farmers and foresters many billions of dollars each year. This particular organism can cause diseases in oranges, grapes, almonds, plums, peaches, alfalfa, oaks, elms and other plants.

"Everyone is quite thrilled," said Dr. Andrew Simpson, a molecular biologist at the Ludwig Institute for Cancer Research in São Paulo, Brazil, and one of the team leaders. "It's probably the biggest ever scientific project in Brazil."

The team has been feted by the president of Brazil and serenaded by orchestras, and a new scientificprize was invented just to be given to the team. It was an achievement for developing nations' scienceas well, Dr. Simpson said, as this was the first complete sequence to come from outside the UnitedStates, the United Kingdom or Japan.

LE FIGARO Jeudi 13 Juillet, 2000

GÉNÉTIQUE Décryptage du génome d’une bactérie ravageant les agrumes brésiliens

Les mécanismes de la virulence dévoilés

L'annonce du décryptag complet du génome de la bactérie Xylella fastidiosa constitue un double événement. Non seuloment, c'est la première fois qu'un micro-organisme pathogène pour les végétaux est sequencé, mais, surtout, ce travail remarquable, publié aujourd'hui dans la revue Nature, est 1'ceuvre d'un consortium de laboratoires brésiliens. Le fait que ce pays émergentdans le domaine de la bio1ogie se soit impliqué dans ce projet, avec le soutien de I'Institut national de la recherche agronomique, ne doit rien au hasard:la bactérie séquencée est un redoutable ravageur des agrumes et le Brésil, qui produit le tiers des oranges vendues dans le monde, compte bien utiliser ces connaissances pour maîtriser ce fléau.

Le Brésil parmi les grandsLe Brésil parmi les grands

En parvenant à séquencer le génome de la bactérie Xylella fastidiosa, le Brésil se hisse au niveau des puissances << biologiques>> de la planète: Etats-Unis, Grande-Bretagne, France, Japon, Allemagne. L'nitiative est venue, il y a trois ans, de la Fondation pour le soutien de la recherche scientifique et technique de I'Etat de San Paolo (FAPESP). Soucieuse de développer la biologie moléculaire, cette institution qui gère le produit de l'impôt destiné à la recherche, lançait par ce biais une sorte de plan keynesien de relance appliqué à la seience. La FAPESP a fourni à chacun des trente laboratoires qui ont répondu à son appe1 d'offres un séquenceur dont le prix unitaire avoisine les 700 000 francs. Ces efforts ont payé. Mieux, les Etats-Unis viennent de commander aux Brésiliens le séquençage d'une souche de X.fastidiosia qui s'attaque à leurs vignobles. Et qui pourrait bien un jour menacer l'Europe et la France. Pas étonnant que ce grand pays ait été invité aux côtés de la Chine, de l'Inde et du Mexique à participer, fin juin, à Bordeaux, à la réunion des ministres de la Recherche du G8.

LE FIGARO Jeudi 13 Juillet, 2000

Wednesday, 12 July, 2000, 18:01 GMT 19:01 UK

Brazil hails scientific first

Xylella fastidiosa was first identified in 1987

By BBC News Online's Jonathan Amos

South American researchers have decoded the first genome for a bacterium that causes disease in plants.

Xylella fastidiosa infects citrus crops and has been known to devastate plantations in Brazil where one third of the world'soranges are now produced.

"The bacteria thrive in the xylem, which are like the veins of the plant transmitting the sap from the roots to the leaves," Dr Simpson said. "Basically, they clog up these tubes so that the extremities and leaves of the plant get undernourished and don't get enough water.

"The fruits become very small and hard, and have no juice in them."

This disease is known as citrus variegated chlorosis (CVC). It was first identified in Brazil in 1987 but it was another six years before X. fastidiosa was shown to be the cause.

Farmers are keen for scientists to develop new ways of combating the disease. In the Sao Paulo region alone, 400,000 people are involved in the citrus business, exporting orange concentrate valued at over $1.5bn a year.

Wednesday, 12 July, 2000, 18:01 GMT 19:01 UK

This disease results in smaller, less juice fruit.

“Genes of Plant Disease Mapped"By JEFF BARNARD, Associated Press Writer

Wednesday, July 12, 2000

For the first time, scientists have reported mapping the genes of a plant disease, an advance that could lead to new approaches to fighting a bacterial scourge that ravages orange groves and other crops.

The work also sheds light on the way bacteria infect both humans and plants and thwart their defenses.

“This sort of information is going to open up crop protection strategies the way genome sequencing is opening up new pharmaceutical strategies to control infectious diseases" in people, said Charles J. Arntzen, president of the Boyce Thompson Institute at Cornell University.

For the first time, scientists have reported mapping the genes of a plant disease, an advance that could lead to new approaches to fighting a bacterial scourge that ravages orange groves and other crops.

The work also sheds light on the way bacteria infect both humans and plants and thwart their defenses.

``This sort of information is going to open up crop protection strategies the way genome sequencing is opening up new pharmaceutical strategies to control infectious diseases'' in people, said Charles J. Arntzen, president of the Boyce Thompson Institute at Cornell University.

Sponsored by the State of Sao Paolo Research Foundation in Brazil, 200 scientists in 34 molecular biology labs worked for two years to sequence the genome of the bacteria Xylella fastidiosa.

New York Times - July 12, 2000

Genes of Plant Disease MappedBy The Associated Press

There is a common misconception that only advanced industrialized nations have the wherewithal and skilled human resources needed to achieve cutting-edge science. This misconception is fanned by the number of researchers from developing countries who find it necessary to obtain their research training abroad - and frequently decide not to return, citing a lack of scientific opportunity. But it is given the lie by a paper published in this issue which describes the result of a project carried out by a consortium of research centres in the state of São Paolo in Brazil to sequence the bacterium Xylella fastidiosa. This bacterium causes a disease that affects citrus fruit and other important crops, resulting in many millions of dollars of damage each year.

As the first public sequence of a free-living plant pathogen, the paper represents a significant scientific milestone. But it also sends a clear political signal, namely both the desire and ability of countries such as Brazil to play in the big league. The sequencing project was deliberately chosen by the project's main funding agency, FAPESP, to play a catalytic role in helping research teams equip themselves for the challenge of the post-genome era. It was also intended to send a signal to Brazil´s young scientists that they do not need to leave the country to engage in world-class science. In both respects, it appears to have succeeded.

Editorial