Computational protocol: Draft Genome Sequence of the Fast-Growing Marine Bacterium Vibrio natriegens Strain ATCC 14048

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Protocol publication

[…] Vibrio natriegens (originally described as Pseudomonas natriegens [] and then Beneckea natriegens []) is a moderately halophilic member of the Harveyi clade () and Vibrio core group () that is commonly found in marine and estuarine coastal waters and sediments. Members of the natriegens species in general are tremendously versatile organoheterotrophs, as they exhibit the ability to utilize a diverse variety of organic substrates as carbon and energy sources (). V. natriegens is also recognized as one of the fastest-dividing organisms currently known, with a documented doubling time of 9.8 min (). This is a growth rate that requires an extremely high rate of protein synthesis, which is accommodated by a higher rRNA gene dose, increases in ribosome numbers, strong rRNA promoters (), and, potentially, codon usage bias (). Its nutritional versatility, rapid doubling time, and the fact that it is nonpathogenic to humans have all encouraged the use of this species in teaching exercises and physiological studies (, ). These characteristics also suggest that if better understood, V. natriegens could become a valuable source for genetic parts or a novel biological chassis capable of rapid biosyntheses for synthetic biological applications ().To begin to investigate this potential, we sequenced the genome of the V. natriegens type strain ATCC 14048 (NBRC 15636, DSM 759) using an Illumina MiSeq benchtop sequencer. The read library (~300-bp inserts) was composed of 15,999,016 2- × 250-bp paired-end reads that resulted in 779× coverage. Assembly of the reads using the Ray de novo assembly software () with a k-mer value of 49 produced 39 scaffolds (>500 bp), and a genome-scale assembly was constructed with Mauve genome alignment software (version 2.3.1; using the closest fully sequenced relative of V. natriegens, Vibrio sp. strain EJY3 (), as a reference scaffold. Gene prediction and annotation were performed using the RAST (Rapid Annotation using Subsystem Technology) server () and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP).The assembled draft genome of V. natriegens ATCC 14048 is 5,131,685 bp in size with 4,587 RAST-server-annotated open reading frames contained within two circular chromosomes. The 3,202,568-bp chromosome I (43.7% G+C; 86.1% coding sequences, 13.3% hypothetical) is composed of 27 supercontigs and contains 11 rRNA operons and at least 103 tRNAs. In comparison, the 1,929,117-bp chromosome II (42.1% G+C; 85.2% coding sequences, 19.5% hypothetical) is composed of 12 supercontigs and contains 1 rRNA operon and at least 21 tRNAs. The genome also harbored seven insertion sequence elements but no retrons. Further analyses are now under way to better elucidate the genetics of V. natriegens and to develop tools to potentially exploit this organism as a platform for rapid biosynthesis. […]

Pipeline specifications

Software tools Mauve, RAST, PGAP
Application Nucleotide sequence alignment
Organisms uncultured marine bacterium