Draft Genome Sequence of Pandoraea sp. Strain SD6-2, Isolated from Lindane-Contaminated Australian Soil.

Pandoraea sp. strain SD6-2 is a δ-hexachlorocyclohexane-degrading bacterial strain isolated from lindane-contaminated soil in Queensland, Australia. The genome of SD6-2 was sequenced to investigate its ability to degrade δ-hexachlorocyclohexane. Here we report the annotated genome sequence of this strain.

GENOME ANNOUNCEMENT

Strain SD6-2 was isolated during a hexachlorocyclohexane (HCH) degradation study in Australia. Among several other strains from soil from Queensland, Australia, contaminated with γ-HCH (also known as the insecticide lindane), this strain was isolated after six cycles of enrichment using 50 ppm δ-HCH as the sole carbon source. Degradation studies using this strain revealed that it partially degrades δ-HCH, although very slowly compared to other known HCH degraders (1). However, given its superior degradation activity compared to other isolates in the study, strain SD6-2 was chosen for genome sequencing.

Genomic DNA of SD6-2 was prepared using the Qiagen Genomic-tip 20/G kit for bacteria, following the manufacturer’s instructions. We sequenced 500-bp fragments using Illumina HiSeq2000 technology at the John Curtin School of Medical Research, Australian National University. The Ray assembler was used to assemble 13,475,774 100-bp paired-end reads using a k-mer length of 63 (2). This assembly generated 51 contigs >500 bp in length, with an N50 value of 198,404 bp. The total size of the assembly was 5.7 Mb, with a GC content of 62.5%. Paired-end information combined 21 of the contigs into 7 scaffolds, making a total of 37 scaffolds or contigs for the assembly.

Annotation of the genome using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) predicted 5,148 protein-coding sequences in SD6-2, of which 1,222 (23.7%) were hypothetical proteins. The current assembly was also predicted to contain 67 tRNA sequences and 4 rRNA clusters. A BLAST search using the 16S rRNA sequence of SD6-2 against the NCBI database revealed 99.8% (1,405-nucleotide [nt] alignment) identity between SD6-2 and Pandoraea sp. The genome size and GC% of SD6-2 are consistent with the only other sequenced Pandoraea genome (Pandoraea sp. B-6, GenBank accession number AKXS00000000); however, further investigation is needed to determine the true identity of SD6-2.

To the best of our knowledge, all currently characterized HCH degraders have been found to degrade HCH via the same degradation pathway, which requires the linA-linF genes (3–6). A BLAST search within the SD6-2 genome using the linA-linF protein sequences (YP_003545302, BAI96793, YP_003544005, YP_003547114, YP_003547119, and BAI98845) of Sphingobium japonicum UT26S from the NCBI database found none of these genes or their homologues in the SD6-2 genome (1). At this stage, strain SD6-2 was again tested for δ-HCH degradation but no degradation activity was observed (S. Pearce, unpublished data). This result, together with the association of the lin genes with IS6100 elements (5, 7, 8), may explain the loss of degradation activity since the first degradation assay.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AQOU00000000. The version described in this paper is version AQOU01000000.