Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate

The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids). A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus 386B but possesses many additional insertion sequence elements.

bacteria with many uses in food processing (1,2). Acetobacter aceti strain 1023, a traditional rice vinegar mash surface isolate (3), was used in pioneering studies of AAB physiology (4). The continual selection of vinegar strains has favored acetic acid/ethanol resistance traits and disfavored wasteful overoxidation, in which acetic acid is lost as CO 2 (5). Whole-genome sequencing of A. aceti 1023 was used to identify adaptations in this highly domesticated vinegar strain.
Genomic DNA libraries were analyzed by 454 GS-FLX pyrosequencing using both fragment (564,984 reads, 140 Mb total) and mate-pair (3-kb insert; 468,069 reads, 66 Mb total) libraries. A hybrid assembly of Sanger and 454 reads using Newbler (version 2.9) furnished 33 scaffolds composed of 193 contigs (Ͼ0.5 kb) and 3.0 Mb total sequence at 72-fold coverage. The scaffolds were ordered with Mauve (version 2.3.1) (10), using the complete genome sequence of Acetobacter pasteurianus 386B (11) as the template. The NCBI Prokaryotic Genome Annotation Pipeline (version 2.5) and BLASTn analysis predicted 2,650 open reading frames, 66 pseudogenes, and 47 functional RNAs. At least eight scaffolds (0.07 Mb total) appeared to originate from plasmids, as judged by the presence of repBA and plasmid partitioning genes. As is typical for the low-copy-number AAB "cryptic" plasmids (12), the plasmid scaffolds contain few genes that clearly confer a phenotype.
Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession no. JEOA00000000. The version described in this paper is the first version, JEOA01000000.

ACKNOWLEDGMENTS
This work was supported by funds from the College of Agriculture at Purdue University and grants from the Danforth Foundation at Washington University, the Herman Frasch Foundation for Research in Agricultural Chemistry (531HF-02), and the National Science Foundation (MCB 0347250 and an REU supplement for J.E.H.) to T.J.K.
We thank the staff of the Genome Institute at Washington University, including Catrina Fronick, Michael Becker, Kim Delehaunty, Kevin Haub, Shelly O'Laughlin, and Brenda Theising, for library construction and DNA sequencing and finishing. We thank the staff of the Purdue University Genomics Core Facility for library construction and DNA sequencing, and Phillip San Miguel and Rick Westerman for advice and assistance with preliminary assemblies. We also thank Koichi Kondo (Mizkan Group Corporation) for the gift of the title strain and Akiko Okamoto-Kainuma (Tokyo University of Agriculture) for guidance.