Complete Genome Sequence of Enterobacter cloacae UW5, a Rhizobacterium Capable of High Levels of Indole-3-Acetic Acid Production

Abstract

We report the complete genome sequence of Enterobacter cloacae UW5, an indole-3-acetic acid-producing rhizobacterium originally isolated from the rhizosphere of grass. The 4.9-Mbp genome has a G+C content of 54% and contains 4,496 protein-coding sequences.

GENOME ANNOUNCEMENT

Members of the Enterobacter genus are Gram-negative facultative anaerobic bacteria commonly found inhabiting the rhizosphere of plants, and they may also be members of the intestinal microflora of humans. Enterobacter cloacae strains are often endophytes capable of biocontrol of plant infectious diseases or production of plant growth-stimulating compounds (1). E. cloacae UW5 was originally isolated from the rhizosphere of reeds in Waterloo, Ontario, Canada (2, 3), and has been shown to produce high levels of indole-3-acetic acid (IAA) (4), a signaling molecule that acts as a bacterial stress response regulator, antimicrobial metabolite, and plant growth stimulant (5). Regulation of IAA by the transcription factor TyrR has been characterized in this strain (4, 6). The genome of E. cloacae UW5 was sequenced to facilitate further insight into the TyrR regulon and the function of IAA in bacterial physiology and bacterial-plant interactions.

Genomic DNA was extracted from an overnight culture grown at 30°C, using the Wizard Genomic DNA purification kit (Promega). A 100-bp paired-end TruSeq library was prepared with an average fragment size of 444 bp and sequenced in a single Illumina HiSeq 2500 lane (McGill University and Génome Québec Innovation Center, Montreal, Canada). A total of 251,715,967 reads were generated, totaling over 51 billion basses. Seqtk (https://github.com/lh3/seqtk) was used to randomly extract a subset of 10 million forward and reverse paired reads, which were then trimmed using Trimmomatic (7) to remove adapters and low-quality sequences. The resulting reads were assessed for sequence quality using FastQC version 0.11.2 (8) before assembly. Genome assembly was performed using a combination of de novo assembly and reference-guided read mapping to a closely related reference genome. An optimal k-mer of 71 was chosen using VelvetOptimiser, which was used for de novo assembly with Velvet version 1.2.10 (9). A total of 83 contigs were generated, with an average of 330-fold coverage and an N₅₀ length of 2,836,112 bp. The same read data were then mapped to the E. cloacae EcWSU1 reference genome (NC_016514) (10) using CLC Genomics Workbench version 8.0.1 (Qiagen) at both low (80% identity and 50% length fraction) and high (90% identity and 90% length fraction) specificity, and the consensus sequences extracted to produce the reference-guided contigs. Contigs from both de novo and reference-guided assemblies were then joined using the CLC Microbial Genome Finishing module to merge overlapping sequences into a single contig. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok).

The E. cloacae UW5 genome consists of a single chromosome that is 4,904,981 bp in length with a G+C content of 54.46%. The genome contains 4,496 genes assigned with protein-encoding function, 77 tRNA genes, and 25 rRNA genes organized into eight rRNA operons.

Nucleotide sequence accession number.

The complete E. cloacae UW5 genome sequence has been deposited in GenBank under the accession number CP011798. The version reported in this paper is the first version.