Complete Genome Sequence of Francisella halioticida Type Strain DSM 23729 (FSC1005)

Here, we announce the complete genome sequence of the Francisella halioticida type strain DSM 23729 (FSC1005), isolated from a diseased cultured giant abalone in Japan in 2005. The genome is composed of a 2,197,430-bp-long circular chromosome, with a G+C content of 31.2%.

ABSTRACT

Here, we announce the complete genome sequence of the Francisella halioticida type strain DSM 23729 (FSC1005), isolated from a diseased cultured giant abalone in Japan in 2005. The genome is composed of a 2,197,430-bp-long circular chromosome, with a G+C content of 31.2%.

ANNOUNCEMENT

In recent years, several novel species of the genus Francisella, neighbors to the category A biothreat agent Francisella tularensis, have been reported (1). These species are found within a wide range of ecological niches, although they have high sequence identity. This emphasizes the importance of obtaining high-quality genomes for the design of highly specific detection assays (2). Francisella halioticida was isolated in Japan from the hemolymph of a diseased cultured abalone (Haliotis gigantea) in 2005 (3). A live culture of the strain was obtained from the DSMZ German collection of microorganisms. The strain was grown and sequenced in two rounds, first to render Illumina reads and later to render PacBio reads. For the first round, the strain was grown on McLeod agar, and its DNA was extracted using the EZ1 kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. A sequencing library was prepared with a Nextera DNA library prep kit and sequenced with the Illumina MiSeq platform, rendering 840,622 paired-end reads using the MiSeq reagent kit v2 (300 cycles). Prior to analysis, the Illumina reads were trimmed with Trimmomatic v0.36 (4) with the settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 and were quality checked with fastqc using default settings. For the second round, the strain was grown on Columbia blood agar containing sea salt. DNA was extracted using the Genomic Tip 100/G kit (Qiagen) following the protocol of the manufacturer and was sent to the Uppsala Genome Center for PacBio sequencing. DNA was sheared to 10 kb using the Hydroshear instrument from Digilab and size selected using a BluePippin instrument on the S1 high-pass 6- to 10-kb cassette. The library was constructed using the SMRTbell template prep kit 1.0, and 163,482 reads were produced on a PacBio RS II instrument using PacBio’s 6th generation of polymerase and 4th generation chemistry. HGAP3 (5), using default settings, generated 113,558 filtered subreads with an N₅₀ value of 7,931 bp, which were assembled with Canu v1.5 setting the genomeSize to 2 Mbp (6). Circlator clean and fixstart (7), with default settings, were used to remove small and completely contained contigs from the assembly, to trim ends, and to set the start position at the dnaA gene. Illumina reads were mapped to the merged chromosome ends with BWA-MEM algorithm v0.7.17 (8) with default settings to verify circularity. A BAM file with Illumina reads mapped to the final assembly, using BWA with the same settings as before, was used as input to two rounds of Pilon (9) using default settings. Annotation of the final assembly was performed using the NCBI Prokaryotic Genome Annotation Pipeline (10, 11).

The final assembly of Francisella halioticida consists of one 2,197,430-bp-long circular chromosome, with a G+C content of 31.18%. The genome contains 2,096 protein-coding sequences, 201 pseudogenes, 10 rRNAs, 40 tRNAs, and 4 noncoding RNAs. As shown earlier (3), F. halioticida DSM 23729 (FSC1005) does not belong to any previously known Francisella clade. This isolate forms a new separate branching clade in the Francisella genus. This updated knowledge is essential for improving assays to be used in epidemiological studies of Francisella sp. (2).

Data availability.

The complete genome sequence for Francisella halioticida DSM 23729 (FSC1005) has been deposited in DDBJ/ENA/GenBank under the accession no. CP022132.1, and the reads have been deposited in the SRA under accession no. PRJNA389776.