Draft Genome Sequence of Xylella fastidiosa subsp. fastidiosa Strain Stag's Leap.

ITALIC! Xylella fastidiosasubsp. ITALIC! fastidiosacauses Pierce's disease of grapevine. Presented here is the draft genome sequence of the Stag's Leap strain, previously used in pathogenicity/virulence assays to evaluate grapevine germplasm bearing Pierce's disease resistance and a phenotypic assessment of knockout mutants to determine gene function.

GENOME ANNOUNCEMENT

Xylella fastidiosa is a Gram-negative xylem-limited bacterium (1, 2) comprising multiple subspecies causing disease in a wide variety of horticultural and landscape perennials (3). Pierce’s disease (PD) of grapevine is caused by strains of X. fastidiosa subsp. fastidiosa. Over the past 15 years, considerable effort has been devoted toward understanding mechanisms of X. fastidiosa subsp. fastidiosa pathogenicity and interactions with the grapevine host (4). Temecula1 (accession no. NC_004556.1) was the first strain of the subspecies to be completely sequenced (5); this sequence serves as a reference for PD research. The complete genome of X. fastidiosa subsp. fastidiosa strain M23 (accession no. NC_010577.1), isolated from almonds in San Joaquin Valley, CA, also was sequenced (6) and is highly similar to that of Temecula1. A third strain of X. fastidiosa subsp. fastidiosa, Stag’s Leap (isolated from grapevine in Napa Valley, CA) (7), has been used to evaluate PD resistant germplasm and in knockout/pathogenicity/virulence assays to elucidate gene function (8). This study fills a critical knowledge gap, the draft genome sequence of strain Stag’s Leap.

For sequencing, Stag’s Leap was cultured in periwinkle wilt medium (9) at 28°C for 14 days. Cells were collected; total genomic DNA was extracted according to a standard procedure (10). Whole-genome sequencing was performed on the Illumina MiSeq platform (Illumina, Inc., San Diego, CA); 6.59 × 106 paired-end reads (301 bp average length) were generated. Sequence reads were assembled de novo with CLC Genomics Workbench (version 7.5), yielding 99 contigs >1,000 bp. The same sequence reads were then mapped to the M23 complete genome using Bowtie 2 version 2.2.6 (11), generating 20 contigs. Finally, contigs from both de novo and mapping methods were combined manually. The final assembled draft genome (750× mean coverage) had a G+C content of 51.7%, with 2,510,798 bp distributed among 15 contigs ranging in size from 1,307 bp to 731,756 bp. All sequences were annotated using the RAST server (http://rast.nmpdr.org/) (12). The chromosomal sequence had 2,756 open reading frames (ORFs) and 55 RNA genes. The Stag’s Leap draft chromosomal sequence corresponds to 99.0% of the M23 genome (2,535,690 bp) and 99.6% of the Temecula1 genome (2,519,802 bp).

Nucleotide sequence accession numbers.

The X. fastidiosa subsp. fastidiosa strain Stag’s Leap whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. LSMJ00000000. The version described in this paper is version LSMJ00000000.1.