Complete Genome Sequence of Hyperthermophilic Archaeon Thermococcus sp. EXT12c, Isolated from the East Pacific Rise 9°N.

We report the genome sequence of Thermococcus sp. EXT12c isolated from a deep-sea hydrothermal vent at the East Pacific Rise 9°N. Microbes in the genus Thermococcus are able to grow anaerobically at high temperature, around neutral pH, and some of them under high hydrostatic pressure.

GENOME ANNOUNCEMENT

We isolated Thermococcus sp. EXT12c from a hydrothermal chimney rock sample collected from a 2496-m depth near the East Pacific Rise 9°N (9°50′40.2″N, 104°17′37.798″W) during the oceanographic cruise EXTREME (October 2001). T. sp. EXT12c is able to grow under anaerobic conditions, at 85°C and pH 6.8 in TRM medium (1). The strain is available in the UBOCC culture collection (Brest, France) under the reference no. UBOCC-M-2417.

We used a phenol-chloroform technique for DNA extraction and the TruSeq DNA PCR-free kit (Illumina, USA) to prepare paired-end sequencing libraries with an average insert size of 550 nt. Whole-genome sequencing at the Marine Biological Laboratory (Woods Hole, MA, USA) using an Illumina MiSeq machine (MiSeq reagent kit v3) produced 1,335,523 2 × 300 bp reads after quality filtering (2). Our de novo assembly with CLC Genomics Workbench v8.5.1 (https://www.qiagenbioinformatics.com/products/clc-genomics-workbench) resulted in a single chromosome with 2,155,760 nt and a GC content of 54.58%. This single chromosome recruited 98.8% of the short reads, with an average coverage of 350×.

The MaGe genome annotation platform (3–14) identified 2,365 coding sequences; a single 16S-23S operon; and 2 5S rRNA, 46 tRNA, and 16 miscellaneous RNA genes. InterProScan identified 1 integrase, 6 transposases, and 3 clustered regularly interspaced short palindromic repeat (CRISPR) loci associated with cas genes (cas, cst, and cmr), suggesting that the strain probably carries two types of CRISPR systems, class I type I and type III (15). These features suggest that the strain has a certain genomic plasticity.

Among the Thermococcus species with published genomes, T. sp. EXT12c is most closely related to T. nautili strain 30-1T (16). These genomes have a DNA-DNA hybridization value of 43.6% and an average nucleotide identity of 91.18%, as predicted with GGDC v2.1 (17–19) and OrthoANI v1.20 (20), respectively.

T. sp. EXT12c possesses some complete metabolic pathways like the glycolysis and amino acid biosynthesis pathways for alanine, asparagine, glycine, glutamate, and tryptophan. To date, only ten Thermococcales, including T. kodakaraensis, T. litoralis, Pyrococcus furiosus, and P. abyssi (21–25), harbor a complete tryptophan biosynthesis pathway.

In this metabolic pathway, a single locus contains genes leading to the synthesis of chorismate, an intermediate for multiple metabolic pathways (TEXT12C_2159 to TEXT12C_2167), and tryptophan (TEXT12C_2174 to TEXT12C_2168, genes trpCDEGFBA). Within the T. kodakaraensis genome, genes that code for tryptophan biosynthesis are present in a single locus too (26). A transcriptomic study showed that the chorismate synthesis is downregulated when T. kodakaraensis is cultivated under high hydrostatic pressure, compared to atmospheric pressure (27). However, in the same study, the gene trpC, labeled TK0252 in T. kodakaraensis, is upregulated, indicating that the strain could continue to produce tryptophan and compensate the decrease of chorismate production under high pressure. Therefore, the regulation of tryptophan biosynthesis in T. sp. EXT12c under high-pressure conditions requires further investigations.

Accession number(s).

This genome sequence has been deposited in DDBJ/ENA/GenBank under the accession no. LT900021. The version described in this paper is the first version.