Complete Genome Sequence of Pandoraea pnomenusa 3kgm, a Quorum-Sensing Strain Isolated from a Former Landfill Site

Abstract

Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of P. pnomenusa strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS SMRT) sequencer high-resolution technology.

GENOME ANNOUNCEMENT

Pandoraea pnomenusa strain 3kgm was isolated from a soil sample obtained from an ex-landfill site in Puchong, Malaysia. Pandoraea spp. are closely related to and are commonly misidentified as Ralstonia spp. or belonging to the Burkholderia cepacia complex. To accurately identify the organism to the genus and species level, 16S rRNA gene-based PCR assays (1), next-generation sequencing, and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (2) were used. The availability of the complete genome of P. pnomenusa strain 3kgm will facilitate research for this strain, as it provides a fundamental molecular evolution study of its genetic foundation especially in clinical microbiology and to avoid the misidentification of a Pandoraea sp.

In the world of unicellular bacteria, signal integration from the bacterial phenotype and bacterial environment form a network of cellular transduction mechanisms to control their gene expression (3). Using lux, gfp, or lacZ acyl homoserine lactone (AHL) biosensor reporter gene fusions or pigment induction, numerous AHL biosensor assays have been developed to facilitate the screening of AHL production (4). The positive quorum-sensing activity of P. pnomenusa strain 3kgm was screened by the AHL biosensor of Chromobacterium violaceum and Escherichia coli [pSB 401] (5, 6).

The PacBio single-molecule real-time (RS SMRT) sequencer is a third-generation sequencing technology with no amplification required (7). By using this PacBio RS SMRT technology and a low-input 10-kb library preparation, the strain 3kgm genome was sequenced and found to be 5,429,297 bp long with 64.72% G+C content in 1 contig, a consensus accuracy of 99.9997%, and 189.56-fold coverage of the genome. The Hierarchical Genome Assembly Process (HGAP) assembler and targeted resequencing pipeline provided by PacBio in the SMRT Portal were employed to derive this single-contig complete closed genome. HGAP consists of preassembly, de novo assembly with Celera Assembler, and assembly polishing with Quiver. Before assembly using Celera assembler (CA) version 7.0 software, the PacBio Rs_PreAssembler.1 module with default minimum subread length of 500 bp, a minimum read quality of 0.80, and a minimum subread length of 5,000 bp was used to perform error correction of the PacBio RS-generated raw reads. The initial genome assembly was further refined through the PacBio RS_Resequencing.1 software (8). With this refined closed genome sequence, gene prediction was performed through PROkaryotic Dynamic programming Gene-finding ALgorithm (Prodigal) (version 2.60) (9), while rRNA genes were predicted with RNAmmer (10) and tRNA genes were predicted with tRNAscan-SE (11). Subsequently, it was annotated with BLASTx against the NCBI-nt/nr updated database and UniProt database (12, 13). Gene prediction resulted in 4,850 open reading frames (ORFs), and a copy each of 5S rRNA, 16S rRNA, 23S rRNA, and tRNA genes were identified.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. CP006900. The version described in this paper is the first version.