Complete Genome Sequence of Campylobacter hepaticus Strain UF2019SK1, Isolated from a Commercial Layer Flock in the United States

The thermophilic Campylobacter species Campylobacter hepaticus is the causative agent of spotty liver disease (SLD) in chickens. This announcement describes the complete genome sequence of C. hepaticus strain UF2019SK1, isolated from the liver of a commercial layer chicken with SLD in the United States.

0.1 M PBS (pH 7.2) solution and subjected to glk gene PCR to confirm the bacterial growth as C. hepaticus before proceeding to DNA extraction.
Genomic DNA was extracted using a Genomic-tip 100/G kit (Qiagen, Inc., Germantown, MD, USA) according to the manufacturer's instructions. The DNA sample was quantified using a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA), and the sample purity and integrity were checked using NanoDrop and pulsed-field gel analysis, respectively. DNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at Genewiz, LLC (South Plainfield, NJ, USA). An ;10-kb library for PacBio Sequel was constructed using the SMRTbell template prep kit version 1.0 (PacBio, Menlo Park, CA, USA). The library was bound to polymerase using the Sequel binding kit version 2.0 (PacBio) and loaded onto a PacBio Sequel instrument using the MagBead kit version 2 (PacBio). Sequencing was performed on a single PacBio Sequel single-molecule real-time (SMRT) cell, using Instrument Control Software version 5.0.0.6235, Primary analysis software version 5.0.0.6236, and SMRT Link version 5.0.0.6792. Reads were assembled using HGAP 4 (within the SMRT Link suite) and Canu. Sequencing yielded a total of 45,335 corrected PacBio reads with a read distribution (N 50 ) of 5,346 bp and a total of 1,600,012,565 bp. At this point, the corrected sequences were assembled with the CLC Genomics Workbench software version 20 (Qiagen, Inc.). The initial assembly was performed with referenceguided assembly using C. hepaticus strain HV10 (GenBank accession number NZ _CP031611) as the reference. De novo assembly was used to complete and verify the assembled genome sequence. After obtaining a draft circular genome sequence, the remaining gaps were filled by a primer-walking approach. At this point, the circularized genome sequence of C. hepaticus was annotated using NCBI Prokaryotic Genome Annotation Pipeline (PGAP; https://www.ncbi.nlm.nih.gov/genome/annotation_prok/) (11) and was independently analyzed on the Rapid Annotations using Subsystems Technology (RAST) server (http://rast.nmpdr.org/). (12). Since there were no inconsistencies observed, the PGAP annotation was used as the public-facing version. The SEED viewer (http://pubseed .theseed.org/) (13) was used for subsystem functional categorization of the predicted open reading frames (ORFs) obtained from annotation and initial subsystem assignments with RAST. Default parameters were used for all software, including those used for genome assembly and annotation, unless otherwise specified.
Analysis of the C. hepaticus UF2019SK1 chromosome revealed that it consists of a circular chromosome of 1.52 Mb. The sequence mapped to 1,525 open reading frames (ORFs), which included 1,470 coding DNA sequences (CDS), 9 rRNAs, 43 tRNAs, and 3 noncoding RNAs. Similar to other sequenced C. hepaticus strains, the average G1C content of the UF2019SK chromosome was approximately 28%. The SEED viewer assigned about 33% of genes from the predicted ORFs from RAST annotation to a particular biochemical pathway or a subsystem wherein protein metabolism and amino acid utilization pathways made up the two largest subsystems. The genomic data reported in this announcement will be useful in future studies of C. hepaticus pathogenesis and vaccine development.
Data availability. The complete annotated chromosome was deposited in NCBI GenBank under accession number CP065357.1, BioProject accession number PRJNA681575, and BioSample accession number SAMN16960974. The raw reads were deposited in the NCBI SRA under accession number SRX10000234.

ACKNOWLEDGMENT
This study was supported by the USDA National Institute of Food and Agriculture (Animal Health Project, 1023600).