Genome Projects

In 1997 a group of Brazilian scientists had an ambitious idea: to sequence the entire genome of a free-living organism. At that time, only a handful of such genomes had been completely sequenced. This idea was their response to a request from the State of Sao Paulo Research Funding Agency (FAPESP) of something "big" to boost biotechnology research in the state.

They soon realized that they would need a thing called bioinformatics, which is using computers to support the processing and analysis of DNA and protein sequences that a genome project generates. Joao Carlos Setubal and myself, being the closest available bioinformaticians in sight, were immediately contacted. We happily agreed to participate in this first Brazilian genome project, something that changed our life forever. For most participants, the genome was a hallmark. There is your career pre-genome (P.G.) and then there is your career in the genomic era (G.E.)

The work was so intense that we did not have time to publish much about what we did, about all the code we wrote to support this truly distributed project, in which the Internet played a key role. But I list here some related publications: the Nature paper with the first genome, and papers concerning the other, subsequent genome projects. Sequencing genomes has turned into a Brazilian mania, with more than 10 projects finished or underway by early 2002.

The government of the State of Sao Paulo produced a video outlining the main aspects of the first, pioneering project. Check out the Portugese and English versions.

Later, I participated in two other genome projects: Bos indicus anbd Coffea arabica.

Talks

• J. Meidanis. Xylella Genome Project and the Role of Bioinformatics.
  Presented at Uniararas, Araras, Brazil, in October 2019.
  Download presentation

Publications

• J. Salojärvi, A. Rambani et al. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics 56, 721-731 (15 April 2024). Nature reference
• F. C. Canavez et al. Genome sequence and assembly of Bos indicus. Journal of Heredity 103(3), 342-348 (07 February 2012). J. Hered. reference
• A. L. Vettore et al. Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane. Genome Research 13, 2725-2735 (Published online before print November 12, 2003). GR reference
• João Meidanis, Marília D. V. Braga and Sergio Verjovski-Almeida. Whole-Genome Analysis of Transporters in the Plant Pathogen Xylella fastidiosa. Microbiology and Molecular Biology Reviews, June 2002, p. 272-299, Vol. 66, No. 2. MMBR Reference (Abstract)
• A. C. R. da Silva et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459-463 (23 May 2002). Nature reference
• Marília D. V. Braga and João Meidanis. Automatic Annotation of Transport Proteins. Invited speech at the 27th Meeting of the Federation of European Biochemical Societies, Lisbon, June/July 2001. Abstract
• Marília D. V. Braga, Zanoni Dias, Tzy Li Lin, João Meidanis, José A. A. Quitzau, Felipe R. da Silva, and Guilherme P. Telles. Bioinformatics of the Sugarcane EST Project. Genetics and Molecular Biology, Volume 24, pp. 9-15, 2001. A preliminar version follows. Download gunzipped ps
• A. J. G. Simpson et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151-157 (13 July 2000). Nature reference