Draft genome sequence of the naphthalene-degrading bacterium Rhodococcus pyridinivorans RA1 isolated from an industrial soil sample in Mosul, Iraq

TL;DR

This paper presents the draft genome sequence of a bacterium that can break down naphthalene, isolated from industrial soil in Mosul, Iraq.

Contribution

The paper provides the first draft genome of Rhodococcus pyridinivorans RA1, a naphthalene-degrading bacterium from Iraq.

Findings

The draft genome is 5,419,924 base pairs long.

The genome has a GC content of 67.5%.

Abstract

Rhodococcus pyridinivorans RA1 was isolated for the ability to grow on naphthalene from an industrial site near Mosul, Iraq. The draft genome is 5,419,924 bp with a GC content of 67.5%.

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ANNOUNCEMENT

Naphthalene with two aromatic rings is the simplest polycyclic aromatic hydrocarbon (PAH) and is often used as a model for PAH degradation (1, 2). We are interested in the genetic diversity of naphthalene-degrading bacteria from diverse habitats around the world. A scoop of surface soil from an industrial area near Mosul, Iraq (36°27'18.7"N 43°05'31.5"E) was obtained in August 2014. Naphthalene-degrading bacteria were isolated by adding 1.0 g of soil to 50 mL of mineral salts basal (MSB) medium (3), with 3 mM naphthalene and incubated for 5 days at 30°C on a rotary shaker. Following one subculture on the same medium, the cells were plated on LB agar (4). Colonies were streaked for purity on MSB agar with naphthalene, and one isolate was designated as strain RA1.

RA1 genomic DNA was extracted using the DNeasy UltraClean Microbial Kit (QIAGEN, Germantown, MD). The RA1 genome was sequenced by MicrobesNG at the University of Birmingham, UK, using an Illumina HiSeq 2500 with a 250 bp paired-end protocol (Illumina, San Diego, USA) from a DNA library prepared using the Nextera XT Library Prep Kit (Illumina, San Diego, USA) using default parameters except that the input DNA was increased 2-fold, and the PCR elongation time was increased to 45 s. Reads (592, 578) were processed with Trimmomatic version 0.30 (5), with a sliding window quality cutoff of Q15. De novo assembly of the 567,907 processed paired-end reads was with SPAdes 3.5 (6), applying settings of k-mer length of 21, 33, and 55 and enabling single-cell mode as recommended for high GC data sets. QUAST 2.3 software (7) was used to generate assembly statistics. The genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 6.3 (8–10). The SEED tool (11) was used to predict functional genes in subsystem categories. Default parameters were used in the laboratory and computational protocols except where otherwise noted above.

The draft genome sequence of RA1 with 30× coverage is 5,419,924 bp with a GC content of 67.5% distributed within 132 contigs with an N50 value of 122,361 bp and with the largest contig 283,648 bp. PGAP annotated a total of 5,053 CDSs including 4,899 protein coding genes, 54 tRNAs, and 11 rRNAs (five 5S, five 16S, and one 23S). The SEED tool predicted 112 genes for the metabolism of aromatic compounds including genes encoding eight aromatic Rieske dioxygenases and nine meta-aromatic ring cleavage enzymes demonstrating that RA1, like many other rhodococci (12), is a versatile aromatic hydrocarbon degrader.

The Type Strain Genome Server (TYGS) (13) was used to infer the whole-genome-based phylogenetic tree of RA1 utilizing the Genome BLAST Distance Phylogeny (GBDP) method (14) using default settings and the dendrogram inferred with the FastME 2.0 program (15). The genome-to-genome distance (GGDH) bioinformatics tool (16) was used to measure in silico DNA-DNA hybridization (isDDH) values. The best matches to the RA1 genome are the type strains R. pyridinivorans DSM 44555 (accession NZ_LRRI00000000.1) and R. biphenylivorans TG9 (accession NZ_CP022208.1), with isDDH values of 87.4% and 83.5%, respectively.