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The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli

August 2004 , Volume 17 , Number  8
Pages  827 - 836

Claudia B. Monteiro-Vitorello , 1 Luis E. A. Camargo , 1 Marie A. Van Sluys , 2 João P. Kitajima , 3 Daniela Truffi , 1 Alexandre M. do Amaral , 4 Ricardo Harakava , 5 Julio C. F. de Oliveira , 6 Derek Wood , 7 Mariana C. de Oliveira , 2 Cristina Miyaki , 2 Marco A. Takita , 8 Ana C. R. da Silva , 3 , 9 Luis R. Furlan , 10 Dirce M. Carraro , 11 Giovana Camarotte , 3 Nalvo F. Almeida , Jr. , 12 Helaine Carrer , 1 Luiz L. Coutinho , 1 Hamza A. El-Dorry , 9 Maria I. T. Ferro , 6 Paulo R. Gagliardi , 1 Eder Giglioti , 13 Maria H. S. Goldman , 14 Gustavo H. Goldman , 15 Edna T. Kimura , 16 Emer S. Ferro , 16 Eiko E. Kuramae , 10 Eliana G. M. Lemos , 6 Manoel V. F. Lemos , 6 Sonia M. Z. Mauro , 6 Marcos A. Machado , 8 Celso L. Marino , 17 Carlos F. Menck , 16 Luiz R. Nunes , 18 Regina C. Oliveira , 18 Gonçalo G. Pereira , 19 Walter Siqueira , 20 Alessandra A. de Souza , 4 Siu M. Tsai , 21 A. S. Zanca , 19 Andrew J. G. Simpson , 22 Stevens M. Brumbley , 23 and João C. Setúbal 24

1Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; 2Instituto de Biociências, Universidade de São Paulo, R. do Matão, 277, 05508-900, São Paulo, SP, Brazil; 3Alellyx Applied Genomics, R. James Clerk Maxwell 320, 13067-850, Campinas, SP, Brazil; 4Embrapa Recursos Genéticos e Biotecnologia, 70770-900 Brasília-DF, Brazil; 5Instituto Biológico Av. Conselheiro Rodrigues Alves, 1252, 04014-002, São Paulo, SP, Brazil; 6Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Av. Prof. Paulo D, Castellane s/n, 14884-900, Jaboticabal, SP, Brazil; 7Dept. of Microbiology, University of Washington, HSB, H310G, Bx 357242, Seattle, WA 98195-7242, U.S.A.; 8Centro de Citricultura Sylvio Moreira, 13490-000, Cordeirópolis, SP, Brazil; 9Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; 10Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, C. P. 237, 18603-970, Botucatu, SP, Brazil; 11Instituto Ludwig de Pesquisa sobre o Câncer, Rua Prof. Antonio Prudente, 109, 01509-010, São Paulo, SP, Brazil; 12Centro de Ciências Exatas e Tecnologia, Universidade Federal do Mato Grosso do Sul, C. P. 549, 79070-900, Campo Grande, MS, Brazil; 13Centro de Ciências Agrárias, Universidade Federal de São Carlos, C. P. 153, 13600-970, Araras, SP, Brazil; 14Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil; 15Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, 14040-903, Ribeirão Preto, SP, Brazil; 16Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-900, São Paulo, SP, Brazil; 17Instituto de Biociências, Universidade Estadual Paulista, 18618-000, Botucatu, SP, Brazil; 18Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Av. Dr. Cândido Xavier de Almeida Souza, 200, 08780-911, Mogi das Cruzes, SP, Brazil; 19Instituto de Biociências, Universidade Estadual de Campinas, C. P. 6109, 13083-970, Campinas, SP, Brazil; 20Instituto Agronômico de Campinas, C. P. 28, 13001-970, Campinas, SP, Brazil; 21Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, C. P. 96, 13400-970, Piracicaba, SP, Brazil; 22Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, U.S.A.; 23BSES Limited, 50 Meiers Road, Indooroopilly, Queensland, 4068 and The CRC for Tropical Plant Protection, University of Queensland, St. Lucia, Queensland, 4072, Australia; 24Instituto de Computação, C.P. 6176, Universidade Estadual de Campinas, Campinas, SP, 13084-971 Brazil

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Accepted 5 April 2004.

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

© 2004 The American Phytopathological Society