The chemolithoautotrophic betaproteobacterium Tetrathiobacter kashmirensis belongs to the family Alcaligenaceae and is phylogenetically closely related to pathogens such as Taylorella and Bordetella species. While a complete inorganic sulfur oxidation gene cluster, soxCDYZAXWB, is present in its genome, pathogenicity islands or genes associated with virulence, disease, cellular invasion, and/or intracellular resistance are completely absent.Sulfur chemoautotrophy is an ancient metabolism (7). However, ecologically and taxonomically diverse prokaryotes have, over billions of years of evolution, developed myriad mechanisms for inorganic sulfur compound oxidation (4). Tetrathiobacter kashmirensis (reclassified as Advenella kashmirensis), a chemolithoautotrophic betaproteobacterium belonging to the family Alcaligenaceae (3, 5), oxidizes thiosulfate by a poorly understood mechanism called the tetrathionate intermediate (S 4 I) pathway (2-4). Again, though Alcaligenaceae is a monophyletic group of closely related genera (3), its members show extensive ecophysiological diversity and range from soil-dwelling xenobiotic degraders (e.g., Alcaligenes, Achromobacter, etc.) to pathogens of various animal groups (e.g., Bordetella, Taylorella, etc.). As such, the whole-genome shotgun sequence of T. kashmirensis strain WT 001T presented here has two academic uses: (i) in providing a molecular understanding of the S 4 I pathway and (ii) in elucidating the genomic evolution of nonpathogenic Alcaligenaceae vis-à-vis their pathogenic relatives.Whole-genome sequencing was performed with the SOLiD 4 system (Applied Biosystems, Foster City, CA). A total of 33,854,957 mate-paired 50-bp-long reads were utilized for assembly by using a combination of the SOLiD system de novo accessory tools 2.0 software (SOLiD Software) and the CAP3 sequence assembly program (6). The genome was annotated by compiling results obtained from the RAST (Rapid Annotation using Subsystem Technology) server (1) with those derived from manual analyses. In the estimated 4,427,252-bp genome of WT 001 T , 4,563 potential coding sequences (CDSs) were identified, of which 1,029 had no homolog in the nonredundant database. One copy each of the 16S, 23S, and 5S rRNA genes, clustered in a single operon, were identified together with 38 tRNA genes distributed over the genome. The GϩC content of the genome was found to be 54%. During SOLiD-based deep sequencing and contig assembly, a 49,652-bp plasmid, pWTk445, was also identified on the basis of its 99% similarity with the IncP plasmid pBTK445, which was partially sequenced earlier from strain WGT of T. kashmirensis (EU585932). No pathogenicity island (or for that matter, genes associated with virulence or disease, cellular invasion, and/or intracellular resistance) was detected, nor were any genes for motility or chemotaxis, production of toxins or superantigens, quorum sensing, or biofilm formation or adhesion. However, 6 intact or truncated transposase-like genes, 12 phage-related genes, and 63 genes responsible for re...