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Journal of Bacteriology, February 2003, p. 1018-1026, Vol. 185, No. 3
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.3.1018-1026.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa

M. A. Van Sluys,^1* M. C. de Oliveira,¹ C. B. Monteiro-Vitorello,² C. Y. Miyaki,¹ L. R. Furlan,^3, L. E. A. Camargo,² A. C. R. da Silva,^4, D. H. Moon,⁵ M. A. Takita,⁶ E. G. M. Lemos,⁷ M. A. Machado,⁶ M. I. T. Ferro,⁷ F. R. da Silva,⁸ M. H. S. Goldman,⁹ G. H. Goldman,¹⁰ M. V. F. Lemos,⁷ H. El-Dorry,⁴ S. M. Tsai,⁵ H. Carrer,² D. M. Carraro,¹¹ R. C. de Oliveira,¹² L. R. Nunes,¹² W. J. Siqueira,¹³ L. L. Coutinho,² E. T. Kimura,¹⁴ E. S. Ferro,¹⁴ R. Harakava,¹⁵ E. E. Kuramae,¹⁶ C. L. Marino,¹⁷ E. Giglioti,¹⁸ I. L. Abreu,⁷ L. M. C. Alves,⁷ A. M. do Amaral,^6, G. S. Baia,¹⁴ S. R. Blanco,⁴ M. S. Brito,⁹ F. S. Cannavan,⁵ A. V. Celestino,¹³ A. F. da Cunha,¹⁹ R. C. Fenille,¹⁶ J. A. Ferro,^7, E. F. Formighieri,⁵ L. T. Kishi,⁷ S. G. Leoni,¹⁴ A. R. Oliveira,¹ V. E. Rosa Jr.,⁸ F. T. Sassaki,¹⁷ J. A. D. Sena,⁷ A. A. de Souza,^6, D. Truffi,² F. Tsukumo,¹⁹ G. M. Yanai,¹² L. G. Zaros,² E. L. Civerolo,²⁰ A. J. G. Simpson,¹¹ N. F. Almeida Jr.,²¹ J. C. Setubal,²² and J. P. Kitajima^8,22,

Instituto de Biociências,¹ Instituto de Química,⁴ Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo,¹⁴ Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900, Piracicaba,² Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, 13400-970, Piracicaba,⁵ Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, 13490-970, Cordeirópolis,⁶ Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal,⁷ Centro de Biologia Molecular e Engenharia Genética,⁸ Instituto de Biologia,¹⁹ Instituto de Computação, Universidade Estadual de Campinas, 13083-970, Campinas,²² Faculdade de Filosofia, Ciências, e Letras,⁹ Faculdade de Ciencias Farmaceuticas, Universidade de São Paulo, 14040-901, Ribeirão Preto,¹⁰ Instituto Ludwig de Pesquisa Sobre o CÂncer, 01509-010, São Paulo,¹¹ Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, 08780-911, Mogi das Cruzes,¹² Instituto Agronômico de Campinas, 13001-970, Campinas,¹³ Instituto Biológico, 04014-002, São Paulo,¹⁵ Faculdade de Medicina Veterinária e Zootecnia,³ Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, 18603-970, Botucatu,¹⁶ Instituto de Biociências, Universidade Estadual Paulista, 18618-000, Botucatu,¹⁷ Universidade Federal de São Carlos, 13600-970, Araras, São Paulo,¹⁸ Departamento de Computação e Estatistica, Universidade Federal de Mato Grosso do Sul, 79070-900, Campo Grande, Mato Grosso do Sul, Brazil,²¹ Agricultural Research Service, U.S. Department of Agriculture, Parlier, California 93648,²⁰

Received 12 July 2002/ Accepted 16 October 2002

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X. fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X. fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X. fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X. fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

Present address: Empresa Brasileira de Pesquisa Agropecuaria, Cordeiropolis, Brazil.

Present address: Alellyx Applied Genomics, 13067-850, Campinas, Sãao Paulo, Brazil.

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