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NEW GENOMES

Two more bacteria in the sights of ONSA

Researchers are going to decipher genes of the Xylella of the grapevine and of Leifsonia

After having deciphered the genome of Xylella fastidiosa and coming near to the conclusion of the sugarcane, cancer and Xanthomonas axonopodis pv citri genome projects, researchers linked to the Organization for the Sequencing and Analysis of Nucleotides – ONSA, the virtual network of genomic research laboratories created by FAPESP, are beginning the deciphering of the genomes of two other bacteria: the variety of Xylella responsible for the destruction of grapevines, and  of the Leifsonia xyli subsp.xyli, formerly known as Clavibacter, which attacks the stalk of the sugarcane plant. The two projects are being developed under the umbrella of a new program baptized Agronomic and Environmental Genomes.

The project of the sequencing of Xylella of grapevines will be developed in partnership with the Department of Agriculture of the United States (USDA). The bacterium, a close relative of Xylella fastidiosa, is threatening the grapevines of California, a production region of top class wines. Also transported by species of glassy-winged sharpshooter, the grape Xylella provokes the sickness named Pierce, which blocks up the tubes that transport the sap thus causing a reduction of their size, the yellowing of the leaves and finally the death of the plant. The result is an annual loss estimated at around US$ 40 million.

The cooperation agreement between the USDA and FAPESP has already been signed. The two institutions are going to split up an investment of US$ 500,000 in the acquisition of latest generation six machines that will be used in the deciphering of the genome. The results will be made available in August of 2001.

The project of the sequencing of the DNA of the grape Xylella was disputed by North American laboratories. In an attempt to make a deal with the USDA, researchers at the Joint Genome Institute (JGI) of Walnut Creek in California, offered to carry out the reading of the DNA of the bacterium within two weeks, and afterwards they even reduced this time to just one day. However, haste can be the enemy of perfection. Edwin Civerolo, of the Agricultural Research Services (ARS) of the USDA, declared to the newspaper Folha de S. Paulo that “it was never clear how this sequencing could possibly have been done so rapidly”. Furthermore, the team from the JGI did not include in their proposal the commitment to carry out the genome’s annotations, or that is to say, to identify among millions of chemical the “letters”, the make-up of specific genes. This omission scored points in favor of the ONSA network. “Time is a critical factor, but quality and the interpretation of the data are as well”, commented to Folha the person responsible for the international programs of the ASR/USDA, Richard Greene. Brazil won the contest and the JGI remained with the task of sequencing another type of Xylella that attacks peanut plants.

Comparative genomics
The agreement with the North Americans is strategic, since it will place Brazil in a partnership with an institution of the stature of the USDA, a type of Ministry of Agriculture of the United States, and reaffirms the international interest for the functional program of Xylella, a pest that attacks more than 150 plants throughout the world. “We’re not dealing with the sale of a service, but of a piece of research of scientific importance that will allow for comparative genomics of the Xylellas of the grape and the orange, which could help to understand the pathogenicity of each of them”, emphasizes José Fernando Perez, FAPESP’s scientific director.

In the case of the grape Xylella, the Brazilian researchers are going to use the same strategy adopted in the deciphering of the genome of Xanthomonas axonopodis pv citri so in order to facilitate the annotation. “We’re not going to sequence the complete genome”, explains Marie-Anne Van Sluys, of the Biosciences Institute of the University of São Paulo (USP), who – along with Mariana Cabral de Oliveira  – is coordinating the project. The genome of the bacterium which attacks the grapevines must have somewhere between 2.7 million and 3.0 million pairs of bases. Random pieces of the genome will be sequenced, in such a manner as to cover between 1,000 and 4,000 pairs of bases, or that is to say one eighth of the total genome. “Our intention is to get as close as possible to the cure and to move forward in the direction of the disease”, says Marie-Anne.

The results will also allow for an identification of the similarities and differences that might exist between the citrus fruit Xylella and the one of the grapevine and might even confirm if the two bacteria are really two distinct varieties of Xylella, since the current classification was done using conventional bacteriology criteria and not through the sequencing of the genome.

The Leifsonia genome
The program for the sequencing of the genome of Leifsonia xyli subsp.xyli will also be a result of international cooperation. The proposal for a partnership was done by an Australian research institute, a sugarcane producing country that lives with the pest in the thick stalk of the plant. The project will also be co-financed by the Cooperative of the Producers of Sugarcane, Sugar and Alcohol of the State of São Paulo (Copersucar), which had previously shown interest in sponsoring the research. In this case the complete genome of the bacteria will be sequenced, which the researchers suspect must be something in the region of 3 million pairs of bases.

The Leifsonia develops in the same ecological nucleus of the Xylella, but with a distinct host, in the case of the sugarcane, and is transmitted by the sugarcane syrup that stays on the cutting knife at the moment of harvesting. The deciphering of the genome will expose the genes involved with the pathogenicity of the bacterium and allow the identification of the likely genes for the control of the disease. “We want to observe if it has the same standards when in contact with the grape or the orange”, explains Luís Eduardo Aranha Camargo, of the Phytopathology Department of the Luiz de Queiroz College of Agriculture (Esalq) of USP.

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