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Partners in research into the Xylella

Researchers intend to decipher the genetic code of another two bacteria

Researchers in the Onsa (Organization for Nucleotide Sequencing and Analysis) network taking part in the Environmental and Agronomic Genomes project have barely had time to pore over their two current undertakings – deciphering the genetic code of two bacteria, the variant of the Xylella fastidiosa that destroys grapevines and the Leifsonia xyli subsp.xyli, which attacks the stalk of the sugarcane – and have already been requested for two new missions. The members of the virtual network linking the genome research laboratories created by FAPESP were invited by the Joint Genome Institute (JGI), a consortium of American laboratories with its headquarters in Walnut Creek, in California, to help it in the task of deciphering two other Xyllela strains: the one that attacks the peanut and the one that inserts itself into an ornamental shrub popularly known as the rosebay or the oleander (Nerium oleander).

According to the oral agreement settled into at the end of October, the Brazilian responsibility would be the task of annotating the genome of these two strains of the Xylellam, whose sequencing, pure and simple, is being done by the researchers at the JGI. In other words, the Onsa scientists will identify, from among the millions of “chemical letters” (the base pairs) making up the genome, the recipes that regulate the production of proteins, interpreting and analyzing the raw data provided by their Californian colleagues. At the beginning of November, JGI announced that it had just completed the “high-quality sketches” containing 95% of the genetic sequences of these two strains of Xyllela plus another 13 bacteria.

In mid-December, the Brazilian researchers will take advantage of a trip to Davis in California, where they will take part in a workshop with Xylella specialists, to discuss the final details of this new partnership. It remains to establish, in particular, whether, as well as the annotation, the Brazilian researchers will also be responsible for the task of filling the gaps not covered by the sequencing done in the JGI, the 5% of the genetic material not mapped. The cooperation agreement involves no money, merely the exchange of knowledge and effort. “The cooperation invitation is a recognition of the quality of our work. We can do the annotation with no problem, but filling these gaps is a lengthy business. We have deadlines to meet in our projects”, says Marie-Anne Van Sluys, of the Botany Department of the Biosciences Institute at the University of São Paulo (USP), one of the coordinators of the grapevine Xylella project.

“The cooperation is interesting because we will have the opportunity of comparing different lineages of this bacterium”, says Mariana Cabral de Oliveira, a departmental colleague of Marie-Anne’s and also a coordinator of the grapevine Xylella project. “It will be a new challenge. With this interchange, we will be able to produce maps comparing the genes of the all the varieties of the Xyllela we and the Americans have sequenced”, says João Paulo Kitajima, of Campinas State University (Unicamp), biological information technology coordinator of the grape Xylella. In time: the São Paulo researchers were the first in the world the decipher the complete genome of a Xylella variety, the citrus type that causes the yellowing (Citrus Variegated Chlorosis – CVC) that attacks oranges, in an already celebrated piece of work that appeared on the cover of Nature, one of the most prestigious scientific magazines in the world.

JGI’s invitation shows that the relationship with the Onsa network, which began as pure competition, can evolve to a more cooperative level. The recent dispute involving the two centers is worth recalling. In a war of words that extrapolated the laboratories and made the pages of Brazilian newspapers, JGI claimed, a few months ago, that is was the main competitor of the Onsa network in the dispute for the grapevine Xylella sequencing project – a project of great interest, partly financed by the US Department of Agriculture (USDA), which is trying to contain the advance of Pierce’s disease, caused by this bacterium, in California, that country’s main fine wine producing region.

At the time, the institute’s directors even claimed that they would be able to read the bacterium’s DNA in less time than the FAPESP network. First, they said they needed only two weeks to complete the task. Then, they lowered the time to 24 hours. As the JGI didn’t make the commitment to supply the annotation of the genetic material of the grape bacterium, precisely the most analytical and refined part of any effort to reveal the DNA of a living being, the USDA preferred to place it bets on the Onsa.

First results
The grapevine Xylella sequencing project, an investment of US$ 500,000 paid for fifty-fifty by FAPESP and by the USDA, is already showing its first results. By November 16, the five centers coordinating the work of the 20 laboratories involved in the initiative already had 20,375 sequences recorded in the database, almost 40% of the total number planned for mapping during the project. In this type of initiative, the researchers produce more genome sequences than are necessary simply to map a genome superficially. They do this in order to reduce as much as possible or even eliminate sections of DNA not read by the sequencing machines and thus obtain more reliable data.

For this reason, although the Xylella genome has around 2.7 million bases, the researchers will sequence 24 million bases. In practice, this is the same thing as saying that each base of the bacterium’s DNA will be read eight times – rather than just once. By the end of January, all the work should have been completed, leaving room in the sequencers for the Leifsonia DNA, Onsa’s next mission.

JGI, a genomics giant
The Joint Genome Institute (JGI), although run by the University California, is part of the US Department of Energy (DOE). Along the National Institutes of Health (NIHs), the DOE is the second largest US organization involved in the international public consortium running the Human Genome Project. And the JGI is the arm of the DOE that runs the Genome Project and other genome initiatives.

Envisaged in 1996 and formally established the following year, the JGI was born with a mission to combine the strength of three successful research centers involved for more than a decade in the Human Genome Project: the Lawrence Berkeley and Lawrence Livermore national laboratories (both in California) and Los Alamos (in New Mexico). When we say successful, this is no exaggeration. The contributions made by this trio of laboratories in the fields of physical mapping and genome sequencing, their strong points, make the JGI a consortium of the highest scientific pedigree. Just one example to demonstrate the dimension of this giant: in April this year, the JGI published the draft of three human chromosomes, numbers 5, 16, and 19. Genes of these chromosomes are thought to be associated with the occurrence of kidney disease, colon, rectal and prostate cancer, leukemia, hypertension, diabetes, and arteriosclerosis.

The JGI employs 240 people. Half of its employees are located at its headquarters in Walnut Creek and half in the institute’s three laboratories. To cover all the stages in the process of mapping DNA, besides drawing on the services of its three member laboratories, the institute also has partnerships with other national laboratories: Oak Ridge (for genome annotating), Brookhaven (molecular biology) and Pacific Northwest (the study of proteome, the set of genes responsible for forming proteins). Stanford’s Genome Center is another of the JGI’s partners.