Draft Genome Sequence of Chromobacterium aquaticum CC-SEYA-1, a Nonpigmented Member of the Genus Chromobacterium

ABSTRACT

Chromobacterium aquaticum CC-SEYA-1^T, isolated from a spring in Taiwan, shares many characteristics with other members of the genus but also contains auxin biosynthesis genes and does not produce the pigment violacein. Chromobacterium sp. 49, isolated from Brazil, is identified here as C. aquaticum, indicating that this is a cosmopolitan species.

GENOME ANNOUNCEMENT

Chromobacterium aquaticum CC-SEYA-1T is a nonproducer of the purple pigment violacein and was isolated from a mountain spring on the island of Taipei. It was recognized as a new species in 2008 (1). Although there has been some additional information published about this organism, its environmental role is unclear (2), and there are no reports of pathogenesis associated with this bacterium. The genus Chromobacterium has undergone a rapid expansion since 2007 (3–8), and the completion of a collection of genomic sequences of all of the species with standing in the literature will be important in redefining or refining the genus. The genome of C. aquaticum CC-SEYA-1 was sequenced at the Arizona State University CLAS Genomics Core facility using Illumina MiSeq. Genomic DNA was sheared to approximately 600-bp fragments using a Covaris M220 ultrasonicator, and Illumina libraries were generated on an Apollo 384 liquid handler (Wafergen) using a Kapa Biosystems library preparation kit (catalog no. KK8201). DNA fragments were end-repaired and A-tailed as described in the Kapa protocol. Combined indexes/adapters (catalog no. 520999; Bioo) were ligated onto each sample and multiplexed into one lane. Adapter-ligated molecules were cleaned using AMPure beads (catalog no. A63883; Agencourt Bioscience/Beckman Coulter, Inc.) and amplified with Kapa HIFI enzyme. Libraries were analyzed on an Agilent Bioanalyzer and quantified by quantitative PCR (qPCR) (catalog no. KK4835; Kapa library quantification kit) before multiplex pooling and sequencing in a 2 × 300 paired-end (PE) flow cell on the MiSeq platform (Illumina). Adapters were computationally segregated and trimmed in the Illumina BaseSpace pipeline. The Velvet assembly tool (BaseSpace) was used for signal processing and partial sequence assembly. The sequence is 63.51% G+C and consists of 4,997,664 bp distributed over 171 scaffolds (≥0 bp), 117 of which are larger than 1 kbp. The largest contig is 311,811 bp, the N₅₀ is 88,237 bp, and the N₇₅ is 44,928 bp, with a sequence coverage of 42.03×.

Ab initio gene prediction was performed on the assembly using RAST (http://rast.nmpdr.org/). There are 4,434 predicted genes in the genome, only 48% of which are identifiable in the RAST/SEED servers. Like many of the other Chromobacterium spp., the C. aquaticum genome contains homologs to Mycobacterium virulence operons for protein synthesis, DNA transcription, and quinolinate biosynthesis, siderophores, heme uptake, chitinases, and N-acetylglucosamine transport pathways. Unlike other Chromobacterium spp., the genome contains genes for auxin biosynthesis via the indole-3-acetaldehyde pathway and an AUX1-like permease. Genes are present for the synthesis of enterobactin siderophores, cyanate hydrolysis, lysozyme inhibitors, and heme/hemin uptake systems. The C. aquaticum CC-SEYA-1 genome sequence was compared to reference genomes of Chromobacterium violaceum, Chromobacterium subtsugae, Chromobacterium haemolyticum, Chromobacterium vaccinii, Chromobacterium piscinae, Chromobacterium pseudoviolaceum, and Chromobacterium sp. LK1, LK11, and 49, using the Genome-to-Genome Distance Calculator (GGDC) (9, 10). The C. aquaticum genome is 93.9% homologous with Chromobacterium sp. 49 (11) but less than 30% homologous to the other reference genomes. Chromobacterium sp. 49 thus is an isolate of C. aquaticum.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number MQZY00000000. The version described in this paper is version MQZY01000000.