Bioinformatic characterization of the reduced genome citrus pathogen Ca. Liberibacter asiaticus

2013-05-08T20:29:34Z (GMT) by Surya Saha Magdalen Lindeberg

Ca. Liberibacter asiaticus (Las) is an alpha-proteobacteria vectored by psyllid insects and believed to be the causal agent of citrus greening or Huanglongbing. However, given the difficulty in culturing this organism, much about its biology remains a mystery. Availability of genome sequence data for a single isolate of Las (Duan, 2009), provides an opportunity to gain insights into its biology and mechanisms of adaptation to host and vector through sequence analysis. Using hidden Markov models based on data from related bacteria, transcription factor binding site predictions have been generated to identify genes with potentially coordinated response to various stimuli. Subcellular localization of annotated gene products based on SignalP and LipoP predictions of signal peptide cleavage sites has been an additional focus given the potential importance of exported and surface proteins in physical interactions with the host and vector. Repetitive regions, mapped using RepeatScout and Repeat Masker, are of use in designing diagnostic probes. Future work will involve characterization of genome architecture through identification of genomic regions orthologous to better studied relatives. Data related to Las characterization can be found on the Citrus Greening - HLB Genome Resources website (http://www.citrusgreening.org). This website is designed as a comprehensive online resource and data sharing platform for the citrus greening research community. In addition to the predicted signal peptides, lipoproteins and transcription factor binding sites, links to off-site analyses such as KEGG pathway maps are also included. Users can explore above mentioned features and add novel annotations on the Las genome using the Artemis or GBrowse genome browsers. Guides for genome viewing and links to other genome analysis tools are also available.