Abstract
Here, we report the draft genome sequence of “Candidatus Liberibacter asiaticus” strain FL17, isolated from a huanglongbing (HLB)-affected citrus tree in central Florida. The FL17 genome comprised 1,227,253 bp, with a G+C content of 36.5%, 1,175 predicted open reading frames, and 53 RNA genes.
GENOME ANNOUNCEMENT
“Candidatus Liberibacter asiaticus” is an unculturable alphaproteobacterium associated with citrus huanglongbing (HLB) (yellow shoot disease, also called greening disease), a devastating citrus disease worldwide (1–3). In the United States, “Ca. Liberibacter asiaticus” was first discovered in Florida in 2005 (4). HLB is now found in all citrus-growing regions in Florida. Due to the lack of in vitro culture, the characterization of “Ca. Liberibacter asiaticus” has mainly relied on DNA sequence analyses. A whole-genome sequence of “Ca. Liberibacter asiaticus” (strain Psy62) was first obtained through a metagenomics approach from an infected Asian citrus psyllid in 2009 (5), followed by sequences of multiple strains from different geographical locations (6–9). Here, we report a draft whole-genome sequence of a “Ca. Liberibacter asiaticus” strain directly from an HLB-affected citrus tree in central Florida.
“Ca. Liberibacter asiaticus” strain FL17 was originally collected from a citrus tree showing typical HLB symptoms (yellowing and mottling) in a nursery in Polk County, FL. Total DNA from an infected leaf petiole was extracted and used for whole-genome sequencing, according to a previously developed procedure (6, 7). Briefly, bacterial DNA was enriched using a NEBNext microbiome DNA enrichment kit (New England BioLabs, Inc., Ipswich, MA) and further amplified using the REPLI-g minikit (Qiagen, Inc., Valencia, CA). Sequencing was performed on an Illumina MiSeq platform (Illumina Inc., San Diego, CA).
MiSeq generated a total of 5.17 × 107 reads (mean, 301 bp) or a total of 1.56 × 1010 bp of data. Using the whole-genome sequences of “Ca. Liberibacter asiaticus” strain Psy62 (5) and two “Ca. Liberibacter asiaticus” phages/prophages (SC1 and SC2) (10) as references, a total of 213,418 reads were identified by using the stand-alone BLAST software (11). The sequence reads were collected by using a Perl script. Assembly was carried out by Velvet 1.2.0 (https://www.ebi.ac.uk/~zerbino/velvet/) (12) and the CLC Genomics Workbench 7.5 software, resulting in 3 contigs ranging from 13,921 bp to 1,198,110 bp, with ~50× coverage. The draft FL17 genome sequence comprised 1,227,253 bp, with a G+C content of 36.5%. Annotation through the RAST server (http://rast.nmpdr.org) (13) identified 1,175 open reading frames (ORFs) and 53 RNA genes.
The citrus-origin FL17 strain genome had a >99% coverage of the psyllid-origin Psy62 strain genome (1,227,204 bp) (5), and both include an SC1 prophage. However, strain Psy62 was later confirmed to harbor an SC2-like prophage sequence, named FP2 (14). In contrast, other than the genes shared by SC1 and SC2, strain FL17 did not have SC2-specific prophage sequences. Therefore, strain FL17 does not appear have an SC2-like prophage.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JWHA00000000. The version described in this paper is version JWHA01000000.
ACKNOWLEDGMENTS
We thank Greg Phillips for technical support.
This research was partially supported by USDA-ARS project no. 5302-22000-010-D, California Citrus Research Board project 5300-151, Chinese Modern Agricultural Technology Systems (CARS-27), and the Special Fund for Agro-Scientific Research in the Public Interest of China.
The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.
Footnotes
Citation Zheng Z, Sun X, Deng X, Chen J. 2015. Whole-genome sequence of “Candidatus Liberibacter asiaticus” from a huanglongbing-affected citrus tree in central Florida. Genome Announc 3(2):e00169-15. doi:10.1128/genomeA.00169-15.
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