Complete Genome Sequence of Acetobacter tropicalis Oregon-R-modENCODE Strain BDGP1, an Acetic Acid Bacterium Found in the Drosophila melanogaster Gut.

Acetobacter tropicalis Oregon-R-modENCODE strain BDGP1 was isolated from Drosophila melanogaster for functional host-microbe interaction studies. The complete genome comprises a single chromosomal circle of 3,988,649 bp with a G+C content of 56% and a conjugative plasmid of 151,013 bp.

GENOME ANNOUNCEMENT

In Drosophila, Acetobacter species are one of the major commensals of the gut microbiota and contribute to larval growth (1). Furthermore, monocolonization of Drosophila with Acetobacter species significantly reduces host development (2). The first draft sequence of A. tropicalis from Drosophila, published in 2014, consisted of 129 contigs (3). We report here the complete genome sequence consisting of a single chromosome and a conjugative plasmid.

A. tropicalis Oregon-R-modENCODE strain BDGP1 was isolated from a fecal swab. Bacteria were streaked onto nutrient broth agar (BD catalog number 213000) plates, single colonies were amplified in culture, and an aliquot was used for 16S V1 and V4 PCR (4) and sequence identification (5). DNA for sequencing was isolated (6), and whole-genome DNA sequencing was performed by the National Center for Genome Resources (NCGR), Santa Fe, New Mexico, USA, using Pacific Biosciences (PacBio) long reads on the RS II instrument (7). A single-molecule real-time (SMRT) cell library was constructed with 5 to 10 µg of DNA using the PacBio 20-kb protocol. The library was sequenced using P6 polymerase and C4 chemistry with 6-h movie times. Sequencing yielded a total of 78,825 reads with a filtered mean read length of 17,469 bp, totaling 1,377,023,046 bp (>200- and >400-fold coverage for the chromosome and plasmid, respectively). A de novo assembly was constructed using the hierarchical genome assembly process (HGAP2) protocol from SMRT Analysis version 2.0 (8–10). The final contigs were manually trimmed and reviewed to produce a single circular chromosome and a single plasmid. Annotations of protein-encoding open reading frames (ORFs) and noncoding RNAs (ncRNAs) were predicted using the Rapid Annotations using Subsystems Technology (RAST) tool (11) and the GenBank annotation pipeline (12).

The chromosomal genome annotation predicts a total of 3,645 genes, including 3,446 protein-coding genes, 77 RNA genes (including 5 rRNA operons, 58 tRNAs, 1 transfer-messenger RNA, and 3 ncRNAs), and 122 pseudogenes. Of the 3,446 protein-coding genes, 82 are contained within two candidate prophages (29 kb, 31 genes, and 39 kb, 51 genes) characterized by genes encoding tailed phage morphogenetic, portal, and terminase large subunit proteins and bounded by genes encoding phage lysin (lysozyme) and integrase. The candidate prophages are only 1.7% of the genome. Additionally, the genome contains a single plasmid, pAtBDGP1A (151,013 bp), with a predicted G+C content of 52%. The plasmid contains 145 candidate protein-coding genes. Among them are genes essential for conjugation (traA, traG, traW, and traY), plasmid replication (repA, repB, and repC), and likely members of a bacterial transport system (traI/dotC, dotG, dotH, icmB/dotO, and icmL/dotI) (13). The plasmid also encodes virulence proteins for arsenic resistance.

Our sequence is significantly similar to that of A. senegalensis 108B, having a 97% average nucleotide identity (14) with 77% coverage of the genome. A. senegalensis originated from a spontaneous cocoa bean fermentation process (GenBank accession number LN606600). Despite the sequence similarity, phenotypically, our strain belongs to the A. tropicalis species based on its ability to grow on maltose and not grow on 10% ethanol or on yeast extract supplemented with 30% d-glucose (15).

Accession number(s).

The chromosome and plasmid sequences of A. tropicalis Oregon-R-modENCODE strain BDGP1 have been deposited in GenBank under the accession numbers CP022699 and CP022700, respectively.