ABSTRACT
This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%, 2,943 open reading frames (ORFs), and 48 RNA genes.
GENOME ANNOUNCEMENT
Xylella fastidiosa is a phytopathogenic, xylem-limited, and nutritionally fastidious bacterium associated with diseases in many economically important plants (1). In 2009, by fulfilling Koch’s postulates, Chang et al. reported a strain of X. fastidiosa causing leaf scorch disease in blueberry in Georgia, USA, and designated the disease blueberry bacterial leaf scorch (BBLS) (2). BBLS is a growing threat to blueberry production in the southern United States, particularly to the highbush cultivars (Vaccinium corymbosum interspecific hybrids). Based on total sales, the blueberry is among the top fruit commodities in the state of Georgia. The public demand for efficient BBLS disease control is high, which requires knowledge of the pathogen. The nutritionally fastidious nature has been a barrier for X. fastidiosa research based on traditional culture-based methodologies. Many basic biology issues of BBLS bacteria remain unclear. For example, while isolation and enzyme-linked immunosorbent assay (ELISA) testing methods could detect the bacterium, they could not determine the subspecies status of the BBLS strain, which is important information for disease epidemiology (3). However, recent advancements in next-generation sequencing (NGS) technology has opened a new venue to study X. fastidiosa through whole-genome sequencing and analyses. To provide baseline information for further disease study, this project reports a de novo genome assembly of an X. fastidiosa BBLS strain.
Strain BB01 of X. fastidiosa was isolated on periwinkle wilt (PW) medium from a symptomatic blueberry (selection FL86-19) collected from Nahunta, GA. This bacterial strain was triple-cloned and cultured at 28°C for 14 days. Bacterial cells were collected by centrifugation. Total genomic DNA was extracted according to a standard procedure (4). Whole-genome sequencing was performed on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA) with 250-bp paired-end reads. A total of 3.65 × 109 bp of sequences was generated. Sequence reads were interleaved and assembled de novo using CLC Genomics Workbench (version 7.5). The BB01 genome (1,271× coverage) had a G+C content of 51.8%, with 2,517,579 bp distributed among 84 contigs ranging in size from 1,006 bp to 197,455 bp. Annotation was performed by the RAST server (http://rast.nmpdr.org/) (5). The BB01 genome was predicted to have a total of 2,943 open reading frames (ORFs) and 48 RNA genes.
To evaluate the subspecies status of BB01 strain, the sequences of the 16S rRNA gene and nrdA (ribonucleotide reductase subunit A) were retrieved and compared to all available whole-genome sequences of X. fastidiosa, including X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, and X. fastidiosa subsp. pauca in GenBank (version 216) through BLASTn analysis. In all cases, strain BB01 clustered with members X. fastdiosa subsp. multiplex, such as strain M12 (6), indicating that BB01 is a strain of X. fastidiosa subsp. multiplex.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. MPAZ00000000. The version described in this paper is the first version, MPAZ01000000.
ACKNOWLEDGMENTS
We thank G. Phillips, R. Huerta, and S. Vargas for technical assistance.
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. The USDA is an equal opportunity provider and employer.
Footnotes
Citation Van Horn C, Chang C-J, Chen J. 2017. De novo whole-genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 isolated from a blueberry in Georgia, USA. Genome Announc 5:e01598-16. https://doi.org/10.1128/genomeA.01598-16.
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