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The Complete Genome Sequence of ‘Candidatus Liberibacter americanus’, Associated with Citrus Huanglongbing

February 2014 , Volume 27 , Number  2
Pages  163 - 176

Nelson A. Wulff,1 Shujian Zhang,2 João C. Setubal,3 Nalvo F. Almeida,4 Elaine C. Martins,1 Ricardo Harakava,5 Dibyendu Kumar,6 Luiz Thiberio Rangel,3 Xavier Foissac,7 Joseph M. Bové,7 and Dean W. Gabriel2

1Departamento Científico–Fundecitrus, Araraquara, SP, 14807-040, Brazil; 2Plant Pathology Department, University of Florida, Gainesville 32611, U.S.A.; 3Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, 05508-000, Brazil; 4Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil; 5Laboratório de Bioquímica Fitopatológica, Instituto Biológico, São Paulo, SP, 04014-002, Brazil; 6ICBR University of Florida, Gainesville 32610, U.S.A; 7UMR-1332 Biologie du Fruit et Pathologie, INRA, Université Bordeaux Ségalen, Villenave d'Ornon, France

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Accepted 25 October 2013.

Liberibacter spp. form a Rhizobiaceae clade of phloem-limited pathogens of limited host range. Two obligately parasitic species have been sequenced: ‘Candidatus Liberibacter asiaticus’, which causes citrus huanglongbing (HLB) worldwide, and ‘Ca. L. solanacearum’, which causes potato “zebra chip” disease. A third (proposed) species, Liberibacter crescens, was isolated from mountain papaya, grown in axenic culture, and sequenced. In an effort to identify common host determinants, the complete genomic DNA sequence of a second HLB species, ‘Ca. L. americanus’ strain ‘São Paulo’ was determined. The circular genome of 1,195,201 bp had an average 31.12% GC content and 983 predicted protein encoding genes, 800 (81.4%) of which had a predicted function. There were 658 genes common to all sequenced Liberibacter spp. and only 8 genes common to ‘Ca. L. americanus’ and ‘Ca. L. asiaticus’ but not found in ‘Ca. L. solanacearum’. Surprisingly, most of the lipopolysaccharide biosynthetic genes were missing from the ‘Ca. L. americanus’ genome, as well as OmpA and a key regulator of flagellin, all indicating a ‘Ca. L. americanus’ strategy of avoiding production of major pathogen-associated molecular patterns present in ‘Ca. L. asiaticus’ and ‘Ca. L. solanacearum’. As with ‘Ca. L. asiaticus’, one of two ‘Ca. L. americanus’ prophages replicated as an excision plasmid and carried potential lysogenic conversion genes that appeared fragmentary or degenerated in ‘Ca. L. solanacearum’.

© 2014 The American Phytopathological Society