Open Access Short Report

Comparative phylogenomics and multi-gene cluster analyses of the Citrus Huanglongbing (HLB)-associated bacterium Candidatus Liberibacter

Harshavardhan Doddapaneni12, Huihong Liao34, Hong Lin1*, Xianjin Bai3, Xiaolong Zhao5, Edwin L Civerolo1, Michael Irey6, Helvecio Coletta-Filho7 and Gerhard Pietersen8

Author Affiliations

1 USDA-ARS. San Joaquin Valley Agricultural Science Center, 9611 So. Riverbend Avenue, Parlier, CA 93648, USA

2 University of California Davis, Department of Viticulture and Enology, Davis, CA 95616, USA

3 Guangxi Academy of Agricultural Sciences, Nanning, PR China

4 Agricultural College, Guangxi University, Nanning, 530004, PR China

5 Guangxi Citrus Research Institute, Guilin, PR China

6 United States Sugar Corporation, Clewiston, Fl 33440, USA

7 Instituto Agronémico de Campinas, Cordeirópolis, Brazil

8 Citrus Research International c/o University of Pretoria, Pretoria, Republic of South Africa

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BMC Research Notes 2008, 1:72  doi:10.1186/1756-0500-1-72

Published: 28 August 2008

Abstract

Background

Huanglongbing (HLB, previously known as citrus greening), is associated with Candidatus Liberibacter species and is a serious threat to citrus production world-wide. The pathogen is a Gram negative, unculturable, phloem-limited bacterium with limited known genomic information. Expanding the genetic knowledge of this organism may provide better understanding of the pathogen and possibly develop effective strategies for control and management of HLB.

Results

Here, we report cloning and characterization of an additional 14.7 Kb of new genomic sequences from three different genomic regions of the Candidatus Liberibacter asiaticus (Las). Sequence variation analyses among the available Ca. Liberibacter species sequences as well as the newly cloned 1.5 Kb of rpoB gene from different Ca. Liberibacter strains have identified INDELs and SNPs. Phylogenetic analysis of the deduced protein sequences from the cloned regions characterizes the HLB-associated Candidatus Liberibacter as a new clade in the sub-division of the α-proteobacteria.

Conclusion

Comparative analyses of the cloned gene regions of Candidatus Liberibacter with members of the order Rhizobiales suggest overall gene structure and order conservation, albeit with minor variations including gene decay due to the identified pseudogenes. The newly cloned gene regions contribute to our understanding of the molecular aspects of genomic evolution of Ca. Liberibacter.