Draft Genome Sequence of a Xylella fastidiosa Strain Causing Bacterial Leaf Scorch of American Elm in Washington, DC

ABSTRACT

Here, we report the draft genome sequence of Xylella fastidiosa strain ATCC 35873, which was obtained from the American Type Culture Collection and was originally isolated from a symptomatic American elm tree grown in Washington, DC. The ATCC 35873 genome contains 2,454,216 bp and has a GC content of 51.68%.

ANNOUNCEMENT

Xylella fastidiosa is an economically important phytobacterium that affects 595 species across 85 plant families, including monocots and dicots in the Americas, Europe, the Middle East, and Asia (1). It causes bacterial leaf scorch and decline in important landscape trees, including the American elm. To date, complete or draft genome sequences of at least 65 X. fastidiosa strains are publicly available, but only 4 are genome sequences of landscape tree strains, including 2 mulberry strains from Maryland and California (2, 3), 1 sycamore strain from Virginia (4), and 1 red oak strain from Georgia (5). Therefore, additional genome sequences of landscape tree strains are needed to better understand the molecular basis of strain divergence, host specificity, nutrient requirements, geographic distribution, and pathogenicity and to develop genome-based specific detection methods. Here, we report the determination of the draft genome of X. fastidiosa strain ATCC 35873, which was obtained from the American Type Culture Collection. Strain ATCC 35873 was originally isolated from an American elm (Ulmus americana) tree in Washington, DC, that displayed leaf scorch symptoms (6).

Genomic DNA of X. fastidiosa strain ATCC 35873 was extracted from a pure culture grown in periwinkle wilt medium (7) using the blood and tissue kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s instructions. Random shotgun and 3-kb mate-pair libraries of ATCC 35873 were generated and sequenced using Roche 454 GS (FLX Titanium) pyrosequencing, resulting in 129,181 shotgun reads and 70,241 mate-pairs, totaling 212,849,656 bases with an average read length of ~300 bases. After processing by the Newbler gsAssembler v. 2.7, the total number of reads from all libraries was 782,358 aligned reads, with 211,378,854 aligned bases. Read quality had an inferred read error of 0.67%, with 99.96% of bases having Q scores of ≥40. The genome was assembled into 174 contigs using the Newbler Assembler. The average length of all of the contigs was 14,104 bases. The largest contig was 217,042 bases. Among the contigs with >200 bases, the contig N₅₀ value was 103,051 bases. All of the contigs were run through an annotation pipeline using GeneMark.hmm v. 3.05 to predict coding regions based on prior Xylella fastidiosa gene models. A total of 1,538 protein-coding regions or putative genes were predicted. To determine the endpoints of putative protein-coding genes of >149 bases, BLASTp was used for queries against a protein database that included UniProt (v. uniref2013_01) and all previously identified Xylella proteins. Ninety-nine percent of the open reading frames (ORFs) had a ≥90% sequence similarity match with existing X. fastidiosa sequences over the length of the query. The translated protein sequences were processed using InterProScan v. 4.8 for functional annotation and UniProt for additional descriptive information. Selected ORFs that were not consistent with annotated Xylella genes were manually annotated. Predictions of tRNA and rRNA regions were made using tRNAscan-SE v. 1.4 (8, 9) and barrnap v. 0.8, respectively.

The depth of sequencing read coverage per base position was 86× for this draft genome of the X. fastidiosa strain ATCC 35873. The genome contains 2,454,216 bp and has a GC content of 51.68%.

Data availability.

The draft genome sequence was deposited in DDBJ/EMBL/GenBank under the accession number JJOI00000000. The raw reads were deposited in the NCBI SRA under the accession numbers SRR20800146 and SRR20800147.