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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #311421

Research Project: Epidemiology and Management of Pierce's Disease and Other Maladies of Grape

Location: Crop Diseases, Pests and Genetics Research

Title: Whole genome sequencing of Candidatus Liberibacter asiaticus strain A4 from Guangdong, China, and strain HHCA from California

Author
item Zheng, Zheng - South China Agricultural University
item Deng, X - South China Agricultural University
item Chen, Jianchi

Submitted to: International Research Conference on Huanglongbing
Publication Type: Abstract Only
Publication Acceptance Date: 2/8/2015
Publication Date: 11/1/2015
Citation: Zheng, Z., Deng, X., Chen, J. 2015. Whole genome sequencing of Candidatus Liberibacter asiaticus strain A4 from Guangdong, China, and strain HHCA from California. International Research Conference on Huanglongbing. p.49.

Interpretive Summary:

Technical Abstract: “Candidatus Liberibacter asiaticus” is associated with citrus Huanglongbing (HLB) in both China and the United States. While HLB has been known for over a century in Guangdong, China, the disease was first discovered in California in 2012. To better study the “old” and “new” HLBs, whole genomes of “Ca. L. asiaticus” Strain A4 from Guangdong, and Strain HHCA from California were sequenced. The A4 genome was sequenced from DNA of a periwinkle plant infected through dodder transmission from an HLB-affected citrus tree. The HHCA genome was sequenced from DNA isolated directly from infected citrus. To overcome the problem of low bacterial titer and interference from host plant DNA, “Ca. L. asiaticus”-infected plant DNA was first treated with MBD2 protein to increase the bacteria/plant DNA ratio. Then, total DNA was increased through multiple displacement amplification and subjected to Illumina (MiSeq) sequencing. Sequence reads of “Ca. L. asiaticus” were identified through a standalone BLAST search with available “Ca. L. asiaticus” whole genome sequences as queries. Bacterial reads were extracted using a Perl script and assembled using Velvet 1.2.10 on a Linux platform. After annotation by RAST server, the A4 strain was determined to have a genome size of 1,208,625 bp, G+C content of 36.4%, 1,107 predicted open reading frames (ORFs), and 53 RNA genes. The HHCA strain has a genome size of 1,118,244 bp, G+C content of 36.6%, 1,191 ORFs, and 51 RNA genes. Unlike the previously published psyllid-derived genome sequences, the sequences of both A4 and HHCA were derived from DNA extracted directly from plant hosts. Strain A4 is currently maintained in a screen-house in China as a continuous source of “Ca. L. asiaticus” DNA for future research.