Genome of Acetobacter tropicalis DmelCS_006

Draft Genome Sequence of Acetobacter tropicalis, isolated from the Gut of Drosophila melanogaster

Adam J. Dobson, John M. Chaston, David R. Sannino, Peter D. Newell, C.N. Adam Wong, Angela E. Douglas

 Department of Entomology, Cornell University, Ithaca, NY

Bacteria associated with animal gastrointestinal tracts are emerging as strong determinants of host health. Member of the genus Acetobacter are commonly dominant in the community found in the gut of the fruit fly Drosophila melanogaster, facilitating study of the effects of individual species on hosts. Here we present the genome sequence of Acetobacter tropicalis strain DmelCS_006 isolated from the gut of Drosophila melanogaster.

Animals host a great diversity of microbes ('microbiota'), upon which they are dependent for normal function of traits, such as immune function (Ivanov and Honda, 2012) and metabolic regulation (Vijay-Kumar et al., 2010). Recent systemic surveys of microbiota (The Human Microbiome Project Consortium, 2012) now require complementary studies to link function to specific taxa. The fruitfly Drosophila melanogaster hosts a low-diversity microbiota (Chandler et al., 2011; Wong et al., 2011), dominated by Acetobacteria and Lactobacilli, presenting an ideal opportunity for microbe-specific functional studies. We have therefore fully sequenced the genome of Acetobacter tropicalis, a proteobacterium commonly found at high abundance in guts of D. melanogaster.

A. tropicalis was isolated from aseptically dissected guts of D. melanogaster, and maintained at 30° C on M.R.S. medium (de Man et al., 1960).  Cultures were grown shaking at 200 rpm to late-log phase and genomic DNA prepared with the Qiagen DNeasy Blood and Tissue Kit as per the manufacturer’s recommendations.  The Cornell Life Sciences Core Facility performed library preparation for Illumina sequencing.

We used 100-bp paired-end sequencing on an Illumina HiSeq 2000 platform, and obtained sequence data for 17,213,360 read pairs. A total of 15,686,249 reads passed quality filtering, providing us with ~840x genome coverage. We assembled the genome using Velvet 1.2.03 by randomly allocating each sequence to one of 6 subset files. Sequences from each subset file were assembled into contigs using kmer lengths of 75-79, aided by predictions of the Velvet Advisor online tool (Zerbino and Birney, 2008); a representative contig file from each subset was used as input in a second velvet run with a kmer length of 77 to create a final assembly that was 3,747,493 bp in length, represented by 129 contigs. Annotation and subsequent analyses were performed using the Rapid Annotation using Subsystem Technology (RAST) server (Aziz et al., 2008).

The RAST server arranged the full genome sequence into 3,654 reading frames, which we searched for in the NCBI non-redundant protein database (NRDB) using BLASTx with a cutoff value of 1.0E-3. The top hits of more than 2,250 of these genes were in other A. tropicalis in the NRDB, with the remainder aligning to proteins in other Acetobacter, Gluconacetobacter and Gluconobacter species. The genome was automatically annotated by SEED (Overbeek et al., 2005) , which predicted no genes for cell adhesion or motility. The genome contains genes for a complete pentose-phosphate pathway, but glycolysis is incomplete due to the absence of Pfk and GPDH enzymes.

The sequence file is available as Download (see sidebar on left).  If you need the data in a different format, please contact us.

Acknowledgements

This work was supported by a NIH grant 1R01GM095372 to AED and Ruth L. Kirschstein NRSA postdoctoral fellowship to PDN (1F32GM099374-01). We thank Peter Schweitzer for assistance with filtering reads and Madeline Galac for assistance installing Velvet.

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